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Accepted Manuscript

Hydrogeological conceptual model of large and complex sedimentary aquifer systems


– Central Kalahari Basin (Botswana)

Moiteela Lekula, Maciek W. Lubczynski, Elisha M. Shemang

PII: S1474-7065(17)30129-8
DOI: 10.1016/j.pce.2018.05.006
Reference: JPCE 2682

To appear in: Physics and Chemistry of the Earth

Received Date: 10 May 2017


Revised Date: 13 December 2017
Accepted Date: 4 May 2018

Please cite this article as: Lekula, M., Lubczynski, M.W., Shemang, E.M., Hydrogeological conceptual
model of large and complex sedimentary aquifer systems – Central Kalahari Basin (Botswana), Physics
and Chemistry of the Earth (2018), doi: 10.1016/j.pce.2018.05.006.

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ACCEPTED MANUSCRIPT

Hydrogeological conceptual model of large and complex sedimentary aquifer

systems – Central Kalahari Basin (Botswana)

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Moiteela Lekulaa. *, Maciek W. Lubczynskia, Elisha M. Shemangb
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Department of Water Resources, Faculty of Geo-information Science and Earth Observation

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(ITC), University of Twente, P.O. Box 217, 7500AA, Enschede, The Netherlands

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b
Department of Earth and Environmental Science, Botswana International University of Science

& Technology, Private bag 16, Palapye, Botswana

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* Corresponding author at:
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Moiteela Lekula (m.lekula@utwente.nl and moiteela17@gmail.com)

P.O. Box 217, 7500AA, Enschede, The Netherlands


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Tel. + 31(0) 53 4874 36


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1 Abstract

2 Successful groundwater resources evaluation and management is nowadays typically undertaken

3 using distributed numerical groundwater flow models. Such models largely rely on

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4 hydrogeological conceptual models. The conceptual models summarize hydrogeological

5 knowledge of an area to be modelled and thereby providing a framework for numerical model

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6 design. In this study, an efficient data integration method for developing hydrogeological

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7 conceptual model of the large and hydrogeologically-complex, Central Kalahari Basin (CKB)

8 aquifer system, was undertaken. In that process, suitability of 3-D geological modelling with

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9 RockWorks code in iterative combination with standard GIS (ArcGIS) was tested. As a result,
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10 six hydrostratigraphic units were identified, their heads and related flow system

11 interdependencies evaluated and hydraulic properties attached. A characteristic feature of the


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12 CKB is a thick unsaturated Kalahari Sand Unit (KSU), that restricts the erratic recharge input to

13 <1 mm yr-1 in the centre to about 5-10 mm yr-1 in the eastern fringe. The analysis of the spatial
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14 distribution of topological surfaces of the hydrostratigraphic units and hydraulic heads of the
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15 aquifers, allowed to identify three flow systems of the three aquifers, Lebung, Ecca and Ghanzi,
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16 all three having similar radially-concentric regional groundwater flow patterns directed towards

17 discharge area of Makgadikgadi Pans. That pattern similarity is likely due to various hydraulic
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18 interconnections, direct or through aquitard leakages, and also due to the presence of the
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19 overlying unconfined, surficial KSU, hydraulically connected with all the three aquifers,

20 redistributing recharge into them. As a result of conceptual modelling, fully 3-D, 6-layer

21 numerical model, with shallow, variably-saturated saturated, unconfined layer is finally

22 recommended as transition from conceptual into numerical model of the CKB. The proposed 3-D

23 geological modelling with RockWorks, turned to be vital and efficient in developing

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24 hydrogeological conceptual model of a large and complex multi-layered aquifer systems. Its

25 strength is in simplicity of operation, in conjunctive, iterative use with other software such as

26 standard GIS and in flexibility to interface with numerical groundwater model.

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27 Keywords: Central Kalahari Basin; Conceptual model; Geographical Information System;

28 Hydrostratigraphy; Karoo; Transboundary aquifer

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29 1. Introduction

30 The successful groundwater resources evaluation and management is nowadays typically

31 done using distributed numerical groundwater models. The reliability of such models is

32 largely determined by realistic hydrogeological conceptual models, which summarize

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33 hydrogeological knowledge of a site to be modelled and thereby providing a framework for

34 numerical model design. According to Anderson et al. (2015), hydrogeological “conceptual

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35 model is a qualitative representation of a groundwater system that conforms to

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36 hydrogeological principles and is based on geological, geophysical, hydrological,

37 hydrogeochemical and other ancillary information”; hence it includes both, the

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38 hydrogeological framework and hydrological system characterization. A conceptual model is
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39 usually presented in a series of cross sections, fence diagrams and tables showing distribution

40 of hydrostratigraphic units and boundary conditions with groundwater flow directions and
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41 hydrogeological parameter estimates. All these, are reconstructed from surface and
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42 subsurface data to help hydrogeologists understand the hydrogeological system behaviour


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43 and support quantitative modelling (Frances et al., 2014). The subsurface geological data

44 such as lithology, structural geology and stratigraphy, are difficult to schematize due to
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45 geological heterogeneity and data scarcity (Trabelsi et al., 2013). Even more difficult is to

46 characterize hydrostratigraphy, hydrogeological parameters, flow systems with their


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47 piezometric surfaces and interactions, all these assessed in this study.


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48 Hydrogeological conceptual model setup usually involves analysis and integration of relevant

49 geological and hydrogeological data using database tool such as a geographical information

50 system (GIS) (Anderson et al., 2015; Trabelsi et al., 2013), although there is no standard

51 widely accepted methodology in that respect (Brassington and Younger, 2010). 3-D

52 geological modelling (Hassen et al., 2016) has not been frequently used in environmental

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53 studies in the past century due to a number of factors, among them high cost of software

54 packages, necessary sophisticated hardware and often shortage of borehole information.

55 However, only recently, the 3-D geological modelling has increasingly been used as a tool for

56 synthesizing all available data types, leading to better understanding and more realistic

57 presentation of a geological settings (Hassen et al., 2016). The demand for 3-D geological

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58 modelling and rapid increase of computer power, resulted in advancement in the 3-D

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59 modelling packages, which allowed development of efficient 3-D geological models on

60 standard desktops (Royse, 2010), making them available to a wider scientific and commercial

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61 community (Raiber et al., 2012). Also this advancement has enabled 3-D geological models

62 to move from the sole use in petroleum and mining industry to all geological disciplines

63
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(Royse, 2010), including hydrogeology (Gill et al., 2011). In groundwater studies, 3-D
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64 geological modelling is used to evaluate complexity of structural geological and
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65 hydrogeological subsurface heterogeneity, which is generally the basis for any

66 hydrogeological conceptual model and therefore a very important step towards building a
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67 numerical distributed groundwater flow models (Bredehoeft, 2002; Robins et al., 2005; Tam
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68 et al., 2014). The 3-D geological models also assist in providing a check on the logic of the

69 hydrogeological conceptualization (Gill et al., 2011), especially important in areas with high
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70 hydrogeological heterogeneity (Tam et al., 2014).


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71 The usefulness of 3-D geological models in hydrogeological conceptualization of aquifers


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72 has been demonstrated worldwide, but only few of them address Africa, especially semi-arid

73 regions, where groundwater is the only source of potable water. In the Northern Africa,

74 (Hassen et al., 2016) constructed 3-D geological model to define the geometry of the

75 Kasserine Aquifer System in Tunisia, which was further used in the development of

76 hydrogeological conceptual model for future development of the 3-D numerical groundwater

77 flow model. In Southern Africa, Lindenmaier et al. (2014) integrated all available geological

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78 information in a 3-D geological model to refine the hydrostratigraphy and to develop a 3-D

79 aquifer map within the Cuvelai-Etosha Basin in Namibia. However, there has not been

80 presented any regional hydrogeological conceptual model of the Central Kalahari Basin

81 (CKB) (Fig. 1), especially not based on the 3-D geological model solution, addressing the

82 complex, multi-layered, geological and hydrogeological CKB system heterogeneity. So far,

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83 only local studies within small parts of the CKB, summarised in the Botswana National

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84 Water Master Plan Review (Snowy Mountains Engineering Corporation and EHES

85 Consulting Engineers, 2006), have been investigated using 3-D geological modelling.

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86 The CKB is very important hydrogeologically to Botswana and neighbouring Namibia, as it

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87 hosts the most productive and exploited transboundary Karoo System Aquifers. A lot of
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88 research in the CKB has been carried out for possible occurrence of oil and coal bedded

89 methane gas, rather than for groundwater potential. These researches included, for example,
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90 studies by Bordy et al. (2010), where they analysed the depositional environment of the

91 Mosolotsane Formation, and other exploration works by international companies like for
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92 example Shell Oil Company. Hydrogeological studies in the CKB have been limited. Farr et
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93 al. (1981) evaluated groundwater resources in Botswana, including the CKB, but their study
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94 did not cover spatial distribution of hydrostratigraphic units. Considering CKB hydrogeology,

95 only few recharge-related studies were published, all referring to CKB fringes (de Vries and
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96 Simmers, 2002; Mazor, 1982; Obakeng et al., 2007; Stadler et al., 2010). There are also some
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97 local, consultancy studies (Geotechnical Consulting Services (Pty) Ltd, 2014; Water Surveys

98 Botswana (Pty) Ltd, 2008; Water Surveys Botswana (Pty) Ltd & Aqualogic (Pty) Ltd, 2007;

99 Wellfield Consulting Services (Pty) Ltd, 2001, 2007, 2009, 2012), presenting local

100 hydrogeological conditions of the CKB, based on borehole data. However, none of them

101 attempted to integrate spatially all the available, fragmented data, to develop hydrogeological

102 conceptual model of the CKB.

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103 The main objective of this study was to develop an efficient method of integrating data from

104 various sources and scales, to develop hydrogeological conceptual model of a large and

105 complex multi-layered aquifer system, such as the CKB. Specific objectives of this study

106 were: 1) to test suitability of 3-D geological modelling tool in: i) integration of data from

107 various sources and scales; ii) modelling of hydrostratigraphic units in large and complex

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108 multi-layered aquifer systems; iii) efficiency of its interfacing with GIS and numerical model;

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109 2) to improve CKB understanding of: i) the spatial distribution of the hydrostratigraphic units

110 and their hydraulic properties; ii) flow systems, their boundaries and interactions between

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111 different hydrostratigraphic units; 3) to adapt the hydrogeological conceptual model to its

112 smooth conversion into regional, numerical model.

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113 2. Description of the CKB study area

The majority of CKB (Fig. 1) is situated in the central part of Botswana (~181,000 km2) and
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115 in the small western part of Namibia (~14,000 km2). The CKB with its boundaries, is
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116 presented in Fig. 1. It is a large-scale hydrogeological basin, which formerly was a catchment
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117 of the fossil Okwa-Mmone River system (de Vries, 1984). Currently it is nearly flat area due

118 to surficial accumulation of eolian sand, known as Kalahari Sand. About 90% of the CKB is
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119 occupied by Kalahari Desert characterised by semi-arid to arid climate because of its position
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120 under the descending limb of the Hadley cell circulation (Batisani and Yarnal, 2010). Most of
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121 the rainfall in the CKB is from convection processes such as instability showers to

122 thunderstorms, several orders of magnitude smaller than the synoptic systems, like the Inter-

123 Tropical Convergence Zone, which control the air-masses supplying the moisture (Bhalotra,

124 1987). Rainfall in the region is highly spatially and temporally variable (Obakeng et al.,

125 2007), with highly localized rainfall showers (Bhalotra, 1987). Almost all rainfall occurs

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126 during the summer, i.e., from September to April. The average annual rainfall ranges from

127 380 mm y-1 in the southwestern to 530 mm y-1 in the north-eastern parts of the CKB.

128 <FIG. 1 HERE>

129 2.1 General geology

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130 Approximately two thirds of the CKB area, i.e. ~128,000 km2, is occupied by the Kalahari

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131 Karoo Basin (KKB) rocks while the remaining ~67,000 km2, by Pre-Karoo rocks (Fig. 2

132 and Fig. 3). The KKB is a sedimentary basin type structure (Catuneanu et al., 2005;

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133 Johnson et al., 1996) with areal extent of 4.5 million km2. It extends over most of

134 Southern African countries (Fig. 2) and is filled with a succession of sedimentary and

135
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volcanic rocks (Table 1), with a maximum vertical thickness of about 12 km (Johnson et
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136 al., 1996).
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137 <FIG. 2 HERE>


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138 2.1.1 Pre-Karoo Groups


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139 There are three Pre-Karoo rock Groups of Proterozoic age (Carney et al., 1994; Key and

140 Ayres, 2000) (Fig. 3): i) Ghanzi Group (weakly metamorphosed purple-red, arkosic
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141 sandstones, siltstones, mudstones and rhythmites) in the north-western part of the study area;
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142 ii) Waterberg Group (Reddish siliciclastic sedimentary rocks, mostly quartzitic sandstones
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143 and conglomerates) in the Southern tip; iii) Transvaal Super Group (interbedded reddish, grey

144 and purple quartzites, carbonaceous siltstones and shales, cherts, limestones, ironstones and

145 volcanics). There are also three Pre-Karoo rock Groups of Archaean age in the CKB (Carney

146 et al., 1994; Key and Ayres, 2000) (Fig 3): i) Gaborone Granite; ii) Kanye Formation

147 composed of felsites; and iii) Okwa Complex composed of porphyritic felsite, granitic gneiss,

148 microgranite and metadolerite.

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149 <FIG. 3 HERE>

150 2.1.2 Karoo Super-Group

151 The Karoo Super Group Formation, in which the CKB groundwater resources occur, has

152 been sub-divided by Smith (1984) into the Lower Karoo (Dwyka, Ecca and Beaufort Groups)

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153 and Upper Karoo (Lebung and Stormberg Groups) based on a regional unconformity (Table

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154 1). Only the Karoo Groups that are present in the CKB and have hydrogeological importance

155 are described. As such, the Dwyka Group is not considered.

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156 Table 1: Stratigraphy and hydrostratigraphy of Karoo Supergroup in the CKB, modified after Smith (1984) to include Pre-Karoo and Kalahari

157 Rocks; the colours correspond to hydrostratigraphic units

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Sub-Basin
DESCRIPTION
Karoo South-East- Northern-Belt Western-
Period Group Kweneng Mmamabula Hydrostratigraphy
Division Central Central Central South-Western Botswana (v)

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AGE (i) (ii)
Kalahari (iii) Kalahari (iv) Kalahari (vi)
Kalahari Sand
CENOZOIC Quaternary Post-Karoo Kalahari Kalahari Group Unit (KSU)

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(Unit1)
Stormberg Basalt
Stormberg
Jurassic Stormberg Lava Group Aquitard (SBA)
Basalts
(Unit 2)

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Lebung Aquifer
Ntane Sandstone Formation Nakalatlou Sst.
Upper (Unit 3)

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MESOZOIC
Karoo Ngwasha Fm.
Triassic Lebung (North East
Only) Mosolotsane
Mosolotsane Fm. Dondong Fm. Inter-Karoo
Fm.

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Pandamatenga Aquitard (IKA)
Fm. (Unit 4)
Upper
Beaufort Kwetla Fm. Thabala Fm. Kwetla Fm. Kule Fm.

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Permian
Boritse Fm. Korotlo Fm. Serowe Fm. Tlapana Fm. Boritse Fm. Otshe Fm.

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Mmamabula Morupule
Fm. Fm.
PALEOZOIC Kweneng Mosomane
Lower Kamotaka Fm Mea Arkose Fm Kweneng Fm.
Ecca Fm. Fm.
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Permian Lower
Karoo Ecca Aquifer
Bori Fm. Makoro Fm. Tswane Fm. Bori Fm. Kobe Fm. (Unit 5)
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Middlepits Fm.
Dwyka Dukwi Fm. Khuis Fm.
Mesoproter
PROTEROZOIC
ozoic Malogong Fm.
Ghanzi Aquifer
Ghanzi Group
(Unit 6)
Pre-Karoo
Basement
ARCHAEAN Waterberg, Transvaal, Gaborone Granite, Kanye Formation, Okwa complex
Aquiclude

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158 Ecca Group

159 The Ecca Group is divided into different formations in different Sub-Basins (Table 1). Generally

160 this group consists of inter-layered sandstone, siltstone, mudstone with carbonaceous mudstones

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161 and coal seams (Smith, 1984). Thicknesses of different units corresponding to different

162 formations vary spatially, so it is difficult to define their boundaries, particularly that most of the

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163 boreholes drilled in the area did not reach the bottom of the Ecca Group. The Ecca Group

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164 represents the principal aquifer in the South-Western Botswana and Kweneng Sub-Basins

165 (Smith, 1984) (Fig. 2 and 3).

166 Beaufort Group


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167 The Beaufort Group follows conformably from the Ecca Group and is characterised by a largely
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168 argillaceous, non-carbonaceous and multi-coloured (yellow, brown, green, greenish grey, purple,

169 cream, white and light grey) sequence of mudstones and subordinate siltstones, with minor fine
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170 to coarse grained sandstone intercalations (Smith, 1984). The Beaufort Group subcrops under the
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171 Kalahari Sand in the southern CKB (Fig. 3).

172 Lebung Group


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173 The Lebung Group lies uncomformably on the Beaufort Group. It is composed of sandstone and
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174 mudstone formations, which have local names in different Karoo Sub-Basins (Table 1, Fig. 2 and
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175 3). In the Lebung Group, there is a downward progression from medium to fine grained, well

176 sorted, reddish to white, massive but fractured sandstones to an argillaceous reddish brown

177 mudstones and siltstones (Smith, 1984). The Ntane and Nakalatlou Sandstone Formations (Table

178 1) are the principal aquifers, with the former covering the majority of CKB (Smith, 1984).

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179 Stormberg Basalt Group

180 This group forms the uppermost, volcanic unit of the Karoo Super Group (Table 1), which has

181 spatially limited extent (Fig. 3). It consists of an extensive, and locally thick (>100 m) sequence

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182 of tholeiitic flood basalts. That basalt is characterised by weathered green to reddish purple,

183 amygdaloidal lava flows, dark grey when fresh (Smith, 1984).

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184 2.1.3 Post-Karoo Group

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185 Kalahari Group

186 Post-Karoo (Table 1), superficial deposits of the Kalahari Group (commonly termed ‘Kalahari

187
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Beds’ or ‘Kalahari Sands’), cover the whole study area and have variable thickness ranging from
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188 about 60 to more than 200 m. This group comprises a discordant and highly variable sequence of

189 loose to poorly consolidated sand, silcrete and calcrete intercalations of variable proportions,
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190 subordinate to minor ferricrete, silcretized/calcretized sandstones and mudstones (Smith, 1984).
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191 The large Kalahari Sand thickness, limits recharge in the CKB (Mazor, 1982).
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192 2.2 Structural geology


193 The principal structural elements in the CKB have been defined using aeromagnetic, seismic and
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194 gravity data interpretation (Haddon, 2005; Hutchins and Reeves, 1980). The major structural
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195 features in the CKB are: the N-S trending Kalahari Line, the NE-SW trending Makgadikgadi
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196 Line, the NE-SW trending Tsau Line and the E-W trending Zoetfontein Fault (Carney et al.,

197 1994) (Fig. 3). The Makgadikgadi and Kalahari Lines are major thrust faults, which originated

198 ~2 Ga ago (Carney et al., 1994). The Kalahari Line defines the western edge of the Kapvaal

199 Craton while the Makgadikgadi Line, the north-western edge of the Zimbabwe Craton (Carney et

200 al., 1994; Key and Ayres, 2000; Pouliquen et al., 2008). The Tsau Line is a series of thrust faults

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201 along the strike of the Ghanzi meta-sediments (Ramokate et al., 2000). The Zoetfontein Fault

202 developed during major orogenic episodes in the Lower Proterozoic Era (Smith, 1984). Previous

203 studies by Dietvorst et al. (1991) and Bureau de Recherches Géologiques et Minières (1991)

204 have clearly indicated that movement of pre-existing structures subsequent to lithification in the

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205 Zoetfontein Fault, together with the development of the complex fracture pattern, plays a

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206 significant role in the hydrogeology of the Karoo strata and has a major influence on the yields

207 of boreholes.

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208 2.3 Hydrogeology

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209 The hydrogeological regime of the CKB study area is significantly influenced by geology. The
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210 principal aquifers in the CKB are: Ecca Aquifer, Lebung Aquifer and the Ghanzi Aquifer (Table

211 1). It is remarkable that despite deep occurrence of groundwater (>60 meters below ground
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212 surface), in majority of the CKB, the main regional groundwater flow (Fig. 4) follows the

213 topography, i.e. it is directed from the higher elevated areas along the water divides in the west,
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214 south and east, towards lowest depression area around Makgadikgadi Pan (de Vries et al., 2000).
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215 There are no permanent surface water bodies in the study area and thus de Vries et al. (2000)

216 characterized the CKB as a closed surface water basin with an internal groundwater drainage
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217 system, outflowing towards a natural discharge area of Makgadikgadi Pans (Fig. 4).
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218 Groundwater replenishment by diffuse recharge is of paramount importance in the CKB since
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219 that recharge dictates the amount of groundwater safe yield that can be extracted sustainably

220 from aquifers. However, the high potential evapotranspiration rates due to large vapour pressure

221 deficit, the thick (typically >60m) sandy unsaturated zone, and abundant ‘thirsty’ Kalahari plants

222 very efficient in taking up unsaturated zone moisture (Lubczynski, 2009), do not favour aquifer

223 replenishment. Such environmental conditions prompted researchers to challenge occurrence of

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224 groundwater recharge. For example de Vries (1984) had ruled out groundwater recharge in the

225 Kalahari stating that the current piezometric surface is a residual-fossil feature, resulting from its

226 decay since the last fluvial period, which ended 12 millennia ago. However, later in his other

227 studies, he admitted few mm per annum recharge occurring at the CKB fringes (de Vries et al.,

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228 2000). Also Mazor (1982) showed active recharge in Kalahari fringes, i.e. in Morwamusu and

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229 Kweneng areas, despite the thick Kalahari Sand of about 100 m. These observations were

230 confirmed by recent environmental tracer and groundwater flow modelling studies, which stated

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231 that CKB recharge is only incidentally present, being restricted to very wet years/seasons (such

232 as for example 1999-2000), occurring every 5-10 years (Obakeng et al., 2007); in the eastern

233
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fringe of the CKB, where the mean annual rainfall is ~ 450 mm, the mean annual recharge is in
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234 order of 5-10 mm yr-1 while in the central CKB where the mean annual rainfall is ~ 350 mm, the

235 mean annual recharge is < 1 mm (de Vries et al., 2000; de Vries and Simmers, 2002; Gieske,
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236 1992; Lubczynski, 2006, 2009; Obakeng et al., 2007; Selaolo, 1998). The recharge in the far
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237 western CKB in Namibia, has not been investigated yet.


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238 Groundwater, wellfield abstractions from aquifers in the CKB, are located in the inhabited

239 fringes of the CKB (Fig. 4) as documented by Snowy Mountains Engineering Corporation and
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240 EHES Consulting Engineers (2006). The main groundwater abstractor in the CKB is the
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241 Debswana Diamond Mining Company (DDMC), at three locations; Jwaneng, Letlhakane and
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242 Orapa mines.

243 <FIG. 4 HERE>

244 The Jwaneng mine, in the South-Eastern part of CKB, utilizes the Jwaneng North Wellfield

245 where groundwater is abstracted from the Ecca aquifer. The Orapa and Letlhakane mines, in the

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246 North-Eastern part of the CKB, have a series of wellfields where groundwater is abstracted from

247 the Lebung Aquifer (Fig. 4). Water supply abstraction for major villages from the Ecca Aquifer

248 in the southern part of the CKB, takes place at Gaothobogwe Wellfield, adjacent to the Jwaneng

249 North Wellfield and at the recently developed Bothapatlou Wellfield. In the eastern part of the

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250 CKB, at the Serowe Wellfield, groundwater abstraction is from the Lebung Aquifer and in the

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251 North-Western at Ghanzi Wellfield, the abstraction is from the Ghanzi Group aquifer (Fig. 4)

252 (Snowy Mountains Engineering Corporation and EHES Consulting Engineers, 2006). There are

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253 also some minor abstractions from all the three aquifers for settlement water supply and livestock

254 watering.

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255 3. Methodology of setting up CKB conceptual model
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256 The hydrostratigraphic unit modelling, system parameterization, flow system analysis,

257 preliminary water balance and hydrogeological boundary definition were used as steps in
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258 development of an efficient method of integrating data from various sources at various scale, for
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259 setting up hydrogeological conceptual model of a large and complex, CKB multi-layered aquifer

260 system.
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261 3.1 Borehole and spatial data


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262 Borehole information, spatial geological data (including shapefiles), geological bulletins and
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263 hydrogeological reports done by groundwater consults were sourced from Botswana Geoscience

264 Institute (BGI, former Department of Geological Survey) and Department of Water Affairs

265 (DWA). The geological shapefiles for Namibia were downloaded online. Water levels were

266 sourced from DWA, DDMC and Directorate of Water Resources Management in Namibia

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267 (DWRM). The digital elevation model (DEM) at 90 m spatial resolution was obtained from

268 Shuttle Radar Topography Mission (SRTM) (Jarvis et al., 2008). The developed borehole

269 database contained altitudes, lithological logs, water strikes and rest levels. Published Botswana

270 geological map (Key and Ayres, 2000) as well as hydrogeological reports from groundwater

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271 consultants (Geotechnical Consulting Services (Pty) Ltd, 2014; Pacific Consultants International

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272 and SANYU Consultants INC, 2002b, a; Water Surveys Botswana (Pty) Ltd, 2008; Water

273 Surveys Botswana (Pty) Ltd & Aqualogic (Pty) Ltd, 2007; Wellfield Consulting Services (Pty)

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274 Ltd, 2001, 2007, 2012) provided additional geological information and hydrogeological data like

275 aquifer transmissivity and hydraulic conductivity.

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276 3.2 Geological modelling and hydrostratigraphic units
277 The RockWorks version 17 software package, further referred to as RockWorks, was used for
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278 geological and hydrogeological data analysis and management, and for modelling and

279 visualization of hydrostratigraphic units in topological surfaces and cross-sections for the CKB
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280 conceptual model setup. The RockWorks, an easy to use software for 3-D modelling of
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281 subsurface geology (Trabelsi et al., 2013) and hydrostratigraphy, handles spatial, surface and

282 subsurface data. It provides several methods of gridding and interpolating borehole data to build
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283 3-D spatial model, including inverse distance, kriging, distance to point and triangulation. In this
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284 study, the inverse distance interpolation method with power two and five km node spacing, was
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285 chosen due to its ability to optimally interpolate faulted surfaces by giving less weight to far

286 distant points, thus representing faulted surfaces better.

287 A six hydrostratigraphic units’ schematization (Anderson et al., 2015) for the CKB system (right

288 column of the Table 1) was deduced and proposed, based on detailed analysis of borehole data

289 and related geological formations, subsurface lithology and groundwater occurrence. For

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290 example, in Mmamabula Sub-Basin, the stratigraphic Lebung Group consisting of Ntane and

291 Mosolotsane Formations, was split into two hydrostratigraphic units, the Lebung Aquifer

292 represented by Ntane Sandstone Formation and the Inter-Karoo Aquitard represented by argillic

293 Mosolotsane Formation combined with underlying Thabala Formation of the Beaufort Group

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294 characterized by similar argillic composition. After systematic identification of the six

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295 hydrostratigraphic units, spatial definition of these units was further elaborated in the

296 RockWorks.

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297 Individual borehole coordinates, elevations, hydrostratigraphic unit intervals, deduced from

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298 borehole lithological logs, and digitised major faults from geological shapefiles were added to
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299 RockWorks Borehole Manager tool for interpolation. The 3-D solid model of hydrostratigraphic

300 units was then generated and analysed. This was an iterative process until the satisfactory
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301 hydrostratigraphic thicknesses replicating their known spatial representation was achieved.

302 Different fault angles were also tested and a 900 block faulting angle was set for all the regional
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303 faults. Also spatial location of boreholes used for hydrostratigraphic unit modelling were
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304 considered adequate to address issues of aquifer wedging and hydrostratigraphic displacement

305 due to faulting as some of them were beyond the CKB model domain. Where borehole
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306 lithological logs were insufficient, spatial extent of the hydrostratigraphic units was constrained
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307 by geological shapefiles, which have been deduced using geophysical methods. For visual
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308 presentation, the vertical interval of hydrostratigraphic units were exaggerated 200 times. The

309 resultant 2-D cross sections, drawn along sections of interest, were then used to visualize the

310 spatial extent of hydrostratigraphic units.

311 The thicknesses of individual hydrostratigraphic units were exported from the 3-D geological

312 model as XYZ files and further used to display and examine their spatial extent using ArcGIS

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313 10.4 GIS software, further referred to as ArcGIS. That data export was done because of ArcGIS

314 superior visual display.

315 3.3 System parameterization

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316 The CKB aquifer transmissivity data (T) were extracted from 358 pumping tests documented in

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317 groundwater consultant reports (Geotechnical Consulting Services (Pty) Ltd, 2000, 2014; Pacific

318 Consultants International and SANYU Consultants INC, 2002b, a; Water Surveys Botswana

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319 (Pty) Ltd & Aqualogic (Pty) Ltd, 2007; Wellfield Consulting Services (Pty) Ltd, 2001, 2007,

320 2012). As log-normally distributed spatial property, the T data were interpolated using inverse

321
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distance of power two. That interpolation was carried out in ArcGIS software. The aquifer
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322 hydraulic conductivities (K) were derived from T, dividing them by corresponding aquifer
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323 thicknesses. The aquifer storage parameters were extracted from 116 piezometric pumping tests

324 data and lithology of borehole logs documented in groundwater consultant reports. The data to
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325 estimate aquitards’ K and unsaturated zone parameters were assigned based also on groundwater
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326 consultancy reports and general literature guidelines addressing hydraulic conductivities of semi-

327 permeable lithological units (Brassington, 1998; Freeze and Cherry, 1979).
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328 3.4 Flow system analysis


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329 Flow system of multi-layered CKB is complex, despite the fact there are no surface water bodies
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330 interacting with groundwater; there are only ephemeral rivers and streams, infiltrating water into

331 subsurface shortly after intense rains. Consequently there is only diffuse rain-recharge, which is

332 erratic and on average in order of only few millimetres per year at most (de Vries et al., 2000;

333 Obakeng et al., 2007). Hydraulic heads for each aquifer were defined from the borehole

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334 groundwater level data acquired from DWA, DDMC and DWRW. The hydraulic heads of each

335 aquifer were spatially interpolated using kriging method in ArcGIS, despite sparsely distributed

336 boreholes in some parts of the CKB. In locations with large separation distances between

337 boreholes, artificial control points were used. The interpolated heads defined potentiometric

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338 maps which further determined groundwater flow directions. The aquifer flow systems, locally

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339 connected with overlying unconfined Kalahari Sand Unit (KSU) are: i) Lebung Aquifer; ii) Ecca

340 Aquifer; iii) Ghanzi Aquifer. In the flow system analysis, particular attention was dedicated not

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341 only to aquifer interactions with KSU but also to interrelations between the three flow systems,

342 each interaction pair regulated by leakance of an intra-aquitard.

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343 3.5 Preliminary water balance
344 The only input of water in the CKB is precipitation. The main output is evapotranspiration and
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345 other two small output contributors are: i) groundwater abstraction for habited areas and for

346 wildlife and ii) groundwater outflow towards Makgadikgadi Pans discharge area (Fig. 4).
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347 3.6 Hydrogeological boundary conditions


348 In definition of boundary conditions, first physical boundaries such as spatial extent of
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349 hydrostratigraphic units, surface topography and major tectonic structures were analysed. Next,

350 the result of that analysis was cross-referenced with the regional potentiometric maps, extending
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351 outside the CKB, to deduce regional flow directions. In case of no distinct physical boundaries,
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352 that analysis allowed to delineate external groundwater outflow boundaries, external no-flow

353 boundaries along (parallel to) major streamline directions and characterize internal boundaries

354 such as preferential flow lines along major fault systems and barriers of groundwater flow.

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355 4. CKB conceptual model

356 4.1 Geological modelling and hydrostratigraphic units


357 The six-hydrostratigraphic units within the Karoo Super Group Formation and the Pre-Karoo

358 rocks are identified based on lithological and hydrogeological analysis and are marked by

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359 different colors in Table 1: i) Kalahari Sand Unit (KSU); ii) Stormberg Basalt Aquitard (SBA);

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360 iii) Lebung Aquifer; iv) Inter-Karoo Aquitard (IKA); v) Ecca Aquifer; and vi) Ghanzi Aquifer.

361 They are also presented spatially in series of hydrostratigraphic cross-sections in Fig. 5 and Fig.

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362 6. These cross-sections present spatial extent and thicknesses of the hydrostratigraphic units,

363 geometric and inter-hydrostratigraphic relationships, particularly around the regional faults.

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364 <FIG.5 HERE>

365 <FIG. 6 HERE>


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366 Kalahari Sand Unit (KSU)


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367 The KSU, is the first surficial unit, composed of sandy, unconsolidated to semi-consolidated
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368 deposits. It is the only hydrostratigraphic unit with continuous spatial extent in the whole CKB.
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369 Its thickness is spatially variable, ranging from 6 m in the western part to more than 100 m in the

370 central and northern parts of the CKB (Fig. 6 and Fig. 7a). The characteristic feature of this unit
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371 is that 80-100% of its thickness is unsaturated so only its bottom part is locally saturated. If
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372 directly underlain by any of the aquifers, i.e. Lebung, Ghanzi or Ecca, then it is in hydraulic

373 contact with that aquifer. The KSU is not productive within the CKB, therefore it is not referred

374 as an aquifer, even though perched saturated units occur in its profile.

375 Stormberg Basalt Aquitard (SBA)

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376 The SBA is a hydrostratigraphic unit non-uniformly distributed, composed of sparsely-fractured

377 basalt (Fig. 3). Its thickness is spatially variable ranging from 0 to ~ 200 m, due to the block

378 faulting and basin morphology (Fig. 6 and Fig.7b). The SBA has been eroded in the southern

379 part of the Zoetfontein Fault, where significant uplifting occurred resulting in a horst structure as

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380 seen in Fig. 6 sections H-H, I-I and J-J. The thickest SBA of more than 200 m, is in the CKB

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381 centre, which likely is a result of sufficient space release after deepening of the basin (Fig. 6

382 sections C-C’ and H-H’ and Fig. 7b). The thick SBA in central part of Zoetfontein Fault zone

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383 can be attributed to significant down-faulting of the graben structure, thus preserving the original

384 stratigraphy of the basin. The SBA is considered as highly heterogeneous aquitard.

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385 Lebung Aquifer

386 The Lebung Aquifer, is one of the most productive aquifers in the CKB. It is composed of dual
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387 porosity sandstone characterized with spatially varying thickness, ranging from zero meters in
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388 the north-western part of the CKB where it wedges out and also in the southern part of the
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389 Zoetfontein Fault where it has been eroded as a result of significant uplifting, to ~230 m in the

390 north-eastern and south-western parts of the CKB (Fig. 7c). The depth of the top of the Lebung
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391 Aquifer is also spatially variable, being significantly influenced by deepening of the basin

392 towards the CKB centre and by regional faulting, mainly by Zoetfontein Fault (Fig. 6), being the
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393 deepest in the central part of the CKB where it also coincides with the thickest SBA. Where
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394 overlain by SBA, the Lebung Aquifer is confined but where the SBA is missing, it is

395 hydraulically connected with the overlying KSU creating one unconfined aquifer (provided KSU

396 is saturated at its bottom part) as can be seen in Fig 6 sections B-B’,C-C’ and H-H’. In the

397 western part of CKB, where IKA is absent, the Lebung Aquifer is hydraulically connected with

398 the underlying Ecca aquifer.

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399 <FIG. 7 HERE>

400 Inter-Karoo Aquitard

401 The IKA, is composed of inter-changing low permeability mudstones and siltstones, underlying

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402 the Lebung Aquifer and overlying the Ecca Aquifer. It has low, spatially variable permeability,

403 ranging from nearly impermeable to semi-permeable. Its thickness is spatially variable, ranging

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404 from zero meters in the north-western and southern part of the CKB, to ~250 m in the central

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405 part (Fig. 7d). The depth to the top of the IKA is also spatially variable and significantly

406 controlled by deepening of the basin towards central CKB and also by regional faults (Fig. 6).

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407 The low permeability of this unit ensures no lateral flow and a very low, vertical groundwater
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408 exchange between the Lebung and the underlying Ecca Aquifers, thus acting as an aquitard

409 confinement to the Ecca aquifer (Snowy Mountains Engineering Corporation and EHES
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410 Consulting Engineers, 2006). Where the IKA is absent, the Ecca Aquifer is in hydraulic contact
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411 with the overlying Lebung Aquifer, but in locations where the Lebung Aquifer and the SBA are
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412 missing, the Ecca Aquifer is hydraulically connected with the KSU.

413 Ecca Aquifer


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414 The Ecca Aquifer hydrostratigraphic unit is composed of an alternating sugary-grained sandstone
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415 with coal seams, characterised by smooth transition between different formations (Smith, 1984).
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416 It has a spatially varying thickness ranging from zero in the north-western CKB where it wedges

417 out, to ~290 m in the southern part of the Zoetfontein Fault, where significant uplifting was

418 followed by erosion of the SBA, Lebung Aquifer and even IKA (Fig. 7e) so that Ecca is directly

419 overlain by KSU. The thickness of the Ecca Aquifer in the north-eastern part of the CKB is

420 uncertain due to limited amount of borehole data penetrating the whole Ecca Aquifer thickness.

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421 Depth to the top of the Ecca aquifer is spatially variable and is largely controlled by deepening of

422 the basin towards central CKB and the graben and horst structures of the Zoetfontein Fault zone

423 (Fig. 6). The Ecca Aquifer is the deepest in the southern part of the CKB around the Zoetfontein

424 graben structure, where all the stratigraphic units of the Karoo Super Group are present,

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425 representing the original Karoo sedimentation (Snowy Mountains Engineering Corporation and

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426 EHES Consulting Engineers, 2006). The Ecca Aquifer is confined where overlain by IKA (Fig.

427 6). Where the IKA is absent, the Ecca Aquifer is hydraulically connected with the overlying

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428 Lebung Aquifer and where the Lebung Aquifer and the SBA are missing, it is hydraulically

429 connected with the KSU creating one unconfined aquifer (Fig. 6). The direct hydraulic contact

430
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between Ecca and Lebung Aquifers can be seen in Fig. 6 in sections D-D’ and I-I’ while between
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431 Ecca Aquifer and KSU in section H-H’ and J-J’.
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432 Ghanzi Aquifer


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433 The Ghanzi Aquifer is a sandwich of fractured arkosic sandstones, siltstone, mudstone and
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434 rhythmite; at nearly all its spatial extent is directly overlain by the KSU, the two being in

435 hydraulic contact. It is only present in the north-western part of the CKB (Fig. 7f). Its thickness
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436 is spatially variable, ranging from zero due to wedging towards centre of CKB, to ~230 m (Fig. 6

437 and Fig. 7f) towards the north-western CKB. The depth to the top of the Ghazi Aquifer is also
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438 spatially variable, shallow where the KSU is the only overlying hydrostratigraphic unit and
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439 deeper towards the basin centre, as can be seen in Fig. 6 sections E-E’ and F-F’.

440 Basement Aquiclude

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441 Basement aquiclude is represented by the impermeable unit underlying the deepest aquifer unit

442 in a given location of the flow system. It can be Dwyka, Waterberg, Transvaal, Gaborone

443 Granite, Kanye Formation or Okwa Complex (Table 1).

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444 4.2 System parameterization
445 The KSU is not a productive aquifer in the CKB, so there are no parametric estimates from

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446 pumping tests. However, that sandy, permeable and relatively homogeneous unit, plays an

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447 important role in redistribution and restriction groundwater recharge to underlying aquifers

448 because of its large thickness. The horizontal and vertical hydraulic conductivities of the KSU,

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449 obtained from Snowy Mountains Engineering Corporation and EHES Consulting Engineers
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450 (2006), range from 1.0 to 15.0 md-1 and from 0.1 to 2.0 md-1 respectively. The SBA is

451 represented by a secondary porosity basalt rock type that has negligible storage (Snowy
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452 Mountains Engineering Corporation and EHES Consulting Engineers, 2006) and low, fracture-

453 based, vertical hydraulic conductivity in order of 3.0x10-4 md-1 (Brassington, 1998; Freeze and
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454 Cherry, 1979). The K of the Lebung aquifer presented in Fig. 8a, varies from less than 0.1 to
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455 more than 10.0 md-1, which is in the range typically associated with sandstones (Brassington,

456 1998; Freeze and Cherry, 1979) while the T, from 10.0 to 100.0 m2d-1 (Fig. 8d). The relatively
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457 uniform K and T in the central part of the CKB of Lebung Aquifer is uncertain due to data
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458 limitation, hence it needs to be optimised during the numerical model simulation. The IKA is
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459 composed of semi-permeable layer sequence of siltstones and mudstones, which can be

460 characterized by a horizontal hydraulic conductivity ranging from 8.6x10-7 to 1.2x10-3 and

461 vertical hydraulic conductivity ten times lower than the horizontal hydraulic conductivity

462 (Brassington, 1998; Freeze and Cherry, 1979). The low IKA vertical K assures limited hydraulic

463 contact between Ecca and Lebung aquifers. The K and T of the Ecca Aquifer (Fig. 8b and Fig.

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464 8e, respectively) are highly spatially variable, ranging from low values in the eastern side of the

465 CKB, to large values in the western side, where locally K>10 md-1 and T>500 m2d-1. The large

466 area with T in range 100-500 m2 d-1 in the north-eastern part of CKB is uncertain due to limited

467 amount of data, hence it needs to be optimised during the numerical model simulation. The

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468 Ghanzi Aquifer is hydraulically connected with KSU. Like in the case of Ecca Aquifer, the K

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469 and T of metamorphic, fractured-arkosic composition changes spatially from low values in the

470 western part to higher in the eastern part (Fig. 8c and 8f, respectively), with K ranging from less

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471 than 0.1 to 10.0 m d-1 and T from 10.0 to 100.0 m2 d-1.

472 <FIG. 8 HERE>

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473 4.3 Flow system, water balance and hydrogeological boundary
474 conditions
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475 4.3.1 Kalahari Sand Unit

476 The potentiometric map of the unconfined Kalahari Sand Unit (KSU) is presented in Fig. 9. This
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477 map considers a number of possibilities regarding KSU hydraulic relation with underlying units.
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478 Where the KSU is underlain by aquifers, such as Lebung, Ecca or Ghanzi, and the potentiometric

479 surface is above the KSU bottom, then the lowest part of the KSU is saturated (continuous
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480 isolines); if the potentiometric surface is below the KSU bottom, then the KSU profile is entirely

481 unsaturated (dashed isolines). If the KSU is underlain by aquitard or aquiclude and the
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482 potentiometric surface is above the KSU bottom, then the lowest part of the KSU is saturated, as
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483 unconfined layer isolated from the bottom; otherwise, the KSU is entirely unsaturated.

484 <FIG. 9 HERE>

485 The flow pattern of the KSU is radially-concentric (Fig. 9). It converges from western, eastern

486 and southern no-flow boundaries defined along the CKB watershed divides, towards the

487 northern, Makgadikgadi Pans groundwater outflow boundary. That pattern, matches also the
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488 pattern of underlain aquifers and the regional pattern of groundwater flow, postulated by de

489 Vries (1984) and de Vries et al. (2000). In the central-eastern part of the CKB, the KSU is

490 saturated, being either on top of the SBA or hydraulically connected with underlain Lebung

491 Aquifer. In the north-western part of the CKB, the KSU is in hydraulic connection with Ghanzi

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492 Aquifer, while the connection with Ecca occurs only within a little strip in the western area.

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493 The thickness of the saturated part of the KSU profile, vary spatially from zero (stripped areas in

494 Fig. 9) to 25 m (KSU thickness map not presented), hence the saturated thickness of the KSU is

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495 non-uniformly distributed. Regarding temporal variability of the saturated KSU thickness, it has

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496 to be noted that after substantial recharge, that thickness may increase, afterwards gradually
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497 declining due to downward leakage to the underlying aquifers or due to groundwater

498 evapotranspiration. In the KSU, there are also localised, perched layers, which however play
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499 negligible role in the CKB flownet system, eventually only in redistribution of recharge;

500 therefore, the Kalahari perched layers are neglected in the regional CKB groundwater flow
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501 model.
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502 4.3.2 Lebung Aquifer


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503 The Lebung Aquifer has a spatially limited extent. Like the KSU, its hydraulic heads show a

504 radially-concentric pattern, converging from western, southern and eastern no-flow boundaries,
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505 towards the northern Makgadikgadi Pans groundwater outflow boundary (Fig. 10). In the
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506 peripheral zone of the CKB, where the Lebung Aquifer is directly overlain by KSU (Fig. 10),

507 they both create one hydraulically connected, unconfined aquifer. That hydraulic connection

508 allows for recharge from the KSU into the Lebung Aquifer. In the remaining area, the Lebung

509 Aquifer is confined by overlaying SBA although according to Smith (1984), there is localized

510 leakage across the SBA due to relatively scarce fracture systems. It is interesting that the

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511 directions of the vertical leakages across the overlying SBA and the underlying IKA, are

512 spatially variable. Those leakage directions depend on the potentiometric surface of the Lebung

513 Aquifer relative to the overlying KSU and underlying Ecca aquifer, while the leakage rates

514 across the SBA and IKA depend on the respective leakances.

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515 <FIG. 10 HERE>

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516 At the southern part of the CKB, the groundwater flow system of the Lebung Aquifer is

517 delimited by graben and horst discontinuity structures of the Zoetfontein Fault zone, schematic

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518 of which is presented in Fig. 11. Considering structural position of the Lebung Aquifer at the

519 northern side of the fault, it is likely that this aquifer is in hydraulic contact across the fault with

520
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the Ecca Aquifer at the southern side, although that connection is uncertain, and requires
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521 additional investigations.

522 <FIG. 11 HERE>


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523 The radially-concentric groundwater flow pattern in the Lebung aquifer (and in KSU) implies its
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524 relatively simple water balance, where the Darcian lateral flow originated from water exchanges
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525 with overlying and underlying layers, is discharged at the northern outflow boundary and also by

526 groundwater evapotranspiration as well as some well abstractions.


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527 4.3.3 Ecca Aquifer


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528 The flow pattern of the Ecca Aquifer is similar to the flow patterns of the Lebung Aquifer and
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529 KSU, i.e. the hydraulic heads show a radially concentric pattern converging from western,

530 southern and eastern no-flow boundaries towards the northern outflow boundary at the

531 Makgadikgadi Pans (Fig. 10). That similarity is influenced by good hydraulic Ecca Aquifer

532 connections with: i) KSU in the southern part, towards south of Zoetfontein Fault (Fig. 9, Fig. 11

533 and Fig. 12) and in the western part (Fig. 12); with ii) Lebung Aquifer wedging at the north-

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534 western part (Fig. 12 as well as the cross-sections in Fig. 6); and with iii) Ghanzi Aquifer

535 towards north-west.

536 The majority of the Ecca Aquifer within the CKB is confined by Inter-Karoo Aquitard (IKA)

537 separating it from Lebung aquifer. The spatially variable vertical, upward or downward, leakage

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538 in the IKA as presented in Fig. 12 is constrained by relative positions of the potentiometric

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539 surfaces of the Ecca and Lebung aquifers and IKA leakance.

540 <FIG. 12 HERE>

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541 It is hypothesized that the Ecca Aquifer (like Lebung) represents laterally closed system. It

542 exchanges groundwater only with overlying layers (and losses some water by groundwater

543
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evapotranspiration and abstractions at wellfields located south of the Zoetfontein Fault, see Fig.
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544 4), so that nearly-all the Ecca groundwater is discharged at the northern outflow boundary while

545 the external boundaries are no-flow boundaries. The physical, wedging boundaries at the north-
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546 western and southern limits are reliable no-flow boundaries. The remaining external boundaries
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547 can be assigned as hydraulic no-flow boundaries along streamlines, in directions perpendicular to
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548 equipotential lines; however, some sections of these boundaries, particularly those under thick

549 IKA, are uncertain as not sufficiently documented by adjacent boreholes. Nevertheless, if there is
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550 some flow across these boundaries, it is expected that it is negligible although at the current state

551 of knowledge that hypothesis cannot be proved or rejected. Once numerical model is setup and
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552 calibrated, that hypothesis can be tested.


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553 4.3.4 Ghanzi Aquifer

554 The Ghanzi Aquifer (Fig. 9), is the only aquifer present in the north-western CKB. In the large

555 part of the CKB extent, it is directly overlain by KSU, so prone to recharge, and it is

556 hydraulically connected with saturated KSU (continuous isolines) forming jointly one

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557 unconfined aquifer. The Ghanzi groundwater flow pattern, like of all other aquifers, is directed

558 towards the northern outflow boundary of the Makgadikgadi Pans. In the south-eastern direction,

559 the Ghanzi Aquifer is hydraulically connected with the Ecca Aquifer (Fig. 6 section E-E’ and

560 Fig. 9) and possibly also with Lebung Aquifer (Fig. 6, G-G). Considering that groundwater flow

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561 direction is parallel to the contacts with Ecca and Lebung aquifers, it is expected that the

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562 groundwater exchange with these aquifers is negligible. This means that all the water recharged

563 through KSU into the Ghanzi Aquifer, except of groundwater evapotranspiration loses and

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564 Ghanzi Wellfield abstraction, is discharged at the northern outflow boundary.

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565 5. Discussion
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566 Systematic integration of various Central Kalahari Basin (CKB) data sets from various sources in

567 the 3-D geological model, resulted in development of the hydrogeological conceptual model of
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568 the CKB (Table 1 and Fig. 13). The first important step in the model setup, was the definition of

569 hydrostratigraphic units. Such definition requires good geological and hydrogeological
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570 knowledge. In this study, geology was pretty well defined from investigation boreholes and from
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571 geological studies of Key and Ayres (2000), Carney et al. (1994) and Smith (1984), although

572 conversion of stratigraphic and lithological units into hydrostratigraphic units was still
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573 challenging due to not always clear regional meaning of Groups, Sub-basins and Formations and
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574 their inter-dependencies. The Table 1, attempted to regulate that issue, proposing six
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575 hydrostratigraphic units on top of the aquiclude basement, namely: Kalahari Sand Unit,

576 Stormberg Basalt Aquitard, Lebung Aquifer, Inter-Karoo Aquitard, Ecca Aquifer and Ghanzi

577 Aquifer.

578 Classification of the hydrogeological system of CKB into six hydrostratigraphic units was crucial

579 for the development of the 3-D, CKB hydrostratigraphic model, presented in the form of cross-

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580 sections in Fig. 6. A comprehensive analysis of the geological formations (Table 1), lithological

581 information from borehole logs and potential groundwater occurrences, were used not only the

582 basis for identifying hydrostratigraphic units but also for defining their spatial extents. This was

583 in contrast to the study by Allen et al. (2008), where hydrostratigraphic units and their spatial

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584 extents, were deduced from borehole lithological descriptions only. In locations with inadequate

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585 borehole information, geological shapefiles (Fig. 3) were used to constrain the spatial

586 distribution of the hydrostratigraphic units and to fill in the missing information in spaces

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587 between borehole logs. This process was achieved through flexible, iterative modelling, applying

588 combination of RockWorks and ArcGIS software.

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589 Utilisation of 3-D geological modelling codes such as RockWorks, is particularly suitable for 3-

590 D hydrostratigraphic models of large scale and complex aquifer systems such as proposed in this
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591 study, as it conveniently integrates available data of lithology, stratigraphy, structural geology,

592 tectonics and most importantly hydrogeology, providing opportunity of exporting any
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593 topological data of any required surface, for follow up numerical models. The RockWorks code,
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594 seems to be handier than software-based, hydrostratigraphic conceptualisation built-in numerical

595 modelling environments such as Groundwater Modelling System (GMS) for example used by
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596 Gurwin and Lubczynski (2005). This is mainly, because 3-D modelling codes such as
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597 RockWorks, are much simpler in operation, requiring much less time to learn, while maintaining
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598 comparable capability i.e.: i) flexibility in data processing (e.g. database and conceptual model

599 can be easily upgraded with new available data at any processing stage), particularly needed for

600 the assessment of hydrostratigraphic information; ii) suitability for handling large data sets

601 without compromising their computation time (Allen et al., 2008); iii) easy interfacing with any

602 follow up numerical modelling code.

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603 In hydrogeological conceptual models, hydraulic properties reflect spatial heterogeneity of a

604 system and determine aquifer flows and aquitard leakages. Therefore, spatial system

605 heterogeneity has to be defined carefully by assigning hydraulic parameters applying all

606 information available for each hydrostratigraphic unit separately. Those parameters are further

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607 used in a numerical model, so will further be confirmed, eventually adjusted, during numerical

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608 model calibration (not part of this study). For the CKB aquifers, hydraulic parameters were

609 assigned mainly based on pumping tests while for the KSU and for aquitards, based on lithology

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610 description of borehole logs. All the assigned hydraulic parameters fell in the ranges of their

611 standard ranges as described in Freeze and Cherry (1979) and Brassington (1998).

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612 In numerical model simulations, so also in setting up conceptual models, the shallowest,

613 unconfined layer, is often meant as the one that is responsible for redistribution of recharge but
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614 not having large importance in lateral groundwater flow (Gurwin and Lubczynski, 2005; Hassan

615 et al., 2014). Such layer, as in the CKB is the KSU, can be optimally modelled by variably-
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616 saturated numerical solutions, for example offered by MODFLOW-NWT unsaturated-zone flow
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617 (UZF1) Package (Niswonger et al., 2006). In that solution, the net recharge is inherently

618 estimated, based on driving forces of precipitation and potential evapotranspiration and
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619 parameterization of surface, unsaturated and saturated zones. In the case of the CKB, the
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620 parameterization of the unsaturated zone, nearly entirely embedded within the KSU, is uncertain
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621 because of its large thickness (typically more than 60 m) and little hydraulic information about it

622 as the majority of investigation studies focusses on layers below the KSU.

623 The large thickness of unsaturated zone, and pretty dense and “thirsty” Kalahari vegetation with

624 world-deepest roots and large potential evapotranspiration, imply large interception, transpiration

625 and evaporation processes (Lubczynski, 2000, 2009), all three restricting the net recharge (Rn)

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626 replenishment of groundwater resources. As a result, the Rn is erratic and if present, then very

627 low, i.e. in order of few mm per year only. Considering that spatial distribution of Kalahari

628 woody vegetation is relatively uniform and that the Kalahari soil is quite homogeneous

629 (Obakeng et al., 2007), it can be assumed that the KSU thickness, plays a major role in spatio-

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630 temporal redistribution of subsurface fluxes so also in Rn. That thickness, as defined in

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631 RockWorks, varies spatially from ~60 m at the eastern fringe, through more than 100 m at the

632 central part of the CKB where recharge is unlikely, to less than 10 m at the western edge of the

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633 CKB, where the largest recharge, possibly more than 10 mm y-1 is expected, although to our

634 knowledge, that recharge has not been validated yet.

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635 In a conceptual model setting, it is important to characterize all groundwater flow systems of a

636 study area. As the saturated part of the unconfined KSU is pretty thin (or not present) and besides
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637 if underlain by any of the aquifers, Lebung, Ecca or Ghanzi (Fig. 9), then they jointly create flow

638 system with that underlying aquifer. This means that in total there are three flow systems in the
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639 study area, Lebung, Ecca and Ghanzi, each of them eventually hydraulically connected with
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640 saturated bottom part of KSU. It is remarkable that all the three flow systems, have similar radial

641 flow pattern, with groundwater moving from external boundaries towards northerly located
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642 Makgadikgadi Pans discharge area (Fig. 4, Fig. 9, Fig. 10 and Fig. 12). Such pattern was also
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643 postulated by de Vries et al. (2000).


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644 Despite similar patterns of the three flow systems, there are substantial differences between their

645 hydraulic heads. Such differences do represent driving force of the vertical leakages across the

646 aquitards. The shallowest, SBA aquitard, is spatially limited. It confines Lebung Aquifer,

647 separating it from KSU. That confinement and related leakage depend on SBA leakance, i.e. on

648 thickness and vertical hydraulic conductivity of the basalt, i.e. fracture openings and density of

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649 fractures (Fig. 10). The Inter-Karoo Aquitard (IKA) has also important hydraulic role

650 constraining leakage between Lebung and Ecca aquifers emphasized by locally large head

651 difference. The IKA is composed of semi-permeable siltstone and mudstone so its vertical

652 hydraulic conductivity is dependent on the lithological composition, i.e. mainly on the

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653 contribution of sandy fraction. It is remarkable that at the majority of the IKA extent, there is

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654 downward leakage because of the higher Lebung Aquifer heads than the Ecca Aquifer heads

655 while the opposite leakage direction occurs only in the central part of the basin (Fig. 12). Such

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656 pattern follows Toth flownet system concept (Toth, 1963) and is typical for the hydraulics of

657 sedimentary basins (Verweij, 1993). Considering parameterisation of the two aquitards for the

658
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future numerical model setup, the leakances are unknown so the preliminary-assigned, lithology-
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659 based leakances have to be calibrated within the numerical model (not part of this study).
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660 The reliability of hydrogeological conceptual models is limited by available data quantity and

661 quality. For example, in the CKB, the Ecca Aquifer thickness is generally uncertain because of
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662 limited number of boreholes penetrating the whole Ecca sequence. This particularly refers to the
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663 locations from central, towards the north and north-eastern part of the CKB, where large

664 deepening of the basin takes place. In these locations, most of the boreholes are terminated either
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665 within the IKA or just after they intersect the Ecca. This problem is mitigated by presence of
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666 sparsely distributed deep exploration boreholes, penetrating the whole Karoo sequence, although
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667 such boreholes are pretty scarce. Nevertheless, Voss (2011) have argued that it is not necessary

668 to bring all the complexity of geology into a descriptive groundwater model system just because

669 real geology “looks” complicated thus bringing more uncertainties, hence the use of the sparsely

670 distributed deep exploration borehole logs is deemed adequate.

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671 Conceptual models serve as the critical background step for assembling numerical models.

672 Therefore a transition between the two should be as smooth as possible. For that purpose, a

673 simplified schematic diagram of the CKB hydrogeological conceptual model next to the

674 corresponding, simplified proposal of numerical model schematisation is presented in Fig. 13. In

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675 that proposal, the only source of water input into the CKB is precipitation. The main water

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676 output is evapotranspiration with other two output contributors being groundwater abstraction for

677 inhabited areas and wildlife and lateral groundwater outflow towards Makgadikgadi Pans’

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678 discharge area.

679 <FIG. 13 HERE>

680
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Transition of hydrogeological conceptual models into numerical models is not straightforward. It
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681 varies with software packages and with their interfacing requirements (Cox et al., 2013). The

682 proposed transition of the CKB conceptual model (Fig. 13a) into numerical model is presented in
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683 Fig. 13b. Considering that transition, still choice can be made for either quasi 3-D or full 3-D
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684 numerical model schematisation (not part of this study). In quasi 3-D solution, there are only
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685 lateral flows in the aquifers and vertical leakages in the aquitards, the latter assumed not to have

686 any storage. According to Anderson et al. (2015), the quasi 3-D numerical models have been
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687 surpassed by time because of such simplifying assumptions. In the case of the CKB, the main

688 disadvantage of the quasi 3-D schematization is that it does not permit for realistic simulation of
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689 the spatial aquifer wedging typical in the CKB and also not for particle tracking option to
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690 determine groundwater residence time. As such, for the numerical modelling of the CKB, a fully

691 3-D numerical schematization is recommended.

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692 6. Conclusions
693 This study has shown that a systematic approach of using 3-D geological modelling code such as

694 RockWorks, is vital when developing hydrogeological conceptual models of complex-multi

695 layered aquifer systems. Its strength is in simplicity of operation and iterative conjunctive use

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696 with other GIS-type of software. The RockWorks code supported by ArcGIS, was useful in

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697 improving understanding of the spatial distribution of the CKB hydrostratigraphic units and their

698 hydraulic properties. Besides, it allowed to define flow system interactions and contributed to

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699 definition of external and internal physical CKB boundaries. Therefore, the methodology

700 presented in this study is highly recommended for development of conceptual models,

701
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particularly of large sedimentary, multi-layered hydrogeological systems.
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702 Acknowledgements
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703 This study is part of the first author’s PhD research, which is supported financially by the
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704 Botswana International University of Science and Technology through Botswana Government

705 grant. Special thanks goes to the Department of Water Affairs in Botswana, Botswana
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706 Geoscience Institution, Debswana Diamond Mining Company and Directorate of Water
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707 Resources Management in Namibia, for providing the geological and hydrogeological data,

708 which made this study possible. Free online databases for geological data for Namibia used in
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709 this study, are also acknowledged.


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FIGURE CAPTIONS WITH COLOR PREFENCE IN BRACKETS

Fig. 1. Location, topography and surface water drainage of the Central Kalahari Basin.

(COLOR)

Fig. 2. Distribution of Karoo Basins in Southern Africa after Johnson et al. (1996). The

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Roman numerals denote the following CKB Kalahari Karoo Sub-Basins: i) Kweneng; ii)

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Mmamabula; iii) South-East Central Kalahari; iv) Northern-Belt Central Kalahari; v)

Western-Central Kalahari; vi) South-Western Botswana. (COLOR)

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Fig.3. The Pre-Kalahari geology of the Central Kalahari Basin, modified after Key and Ayres

(2000) and Carney et al. (1994). (COLOR)

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Fig. 4. General inter-layer groundwater flow pattern and major wellfields in the Central
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Kalahari Basin. (COLOR)
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Fig. 5. Spatial distribution of boreholes used in RockWorks database and locations of 10

selected hydrostratigraphic cross-sections in the study area. (COLOR)


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Fig 6. Hydrostratigraphic cross-sections - vertical dashed lines show locations of faults.


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(COLOR)

Fig. 7. Thickness of the six hydrostratigraphic units in the Central Kalahari Basin. Alphabetic
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letters denotes: a) Kalahari Sand Unit; b) Stormberg Basalt Aquitard; c) Lebung Aquifer; d)
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Inter-Karoo Aquitard; e) Ecca Aquifer; f) Ghanzi Aquifer. (COLOR)


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Fig. 8. Aquifer hydraulic conductivity (K) and transmissivity (T) in the Central Kalahari

Basin: a) Lebung Aquifer K; b) Ecca Aquifer K; c) Ghanzi Aquifer K; d) Lebung Aquifer T;

e) Ecca Aquifer T; f) Ghanzi Aquifer T. (COLOR)

Fig. 9. Hydraulic heads and boundary conditions of an unconfined Kalahari Sand Unit (KSU)

and Ghanzi Aquifer. (COLOR)


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Fig. 10. Hydraulic heads and boundary conditions of Lebung Aquifer. (COLOR)

Fig. 11. Schematic of flow system adjacent to Zoetfontein Fault. (COLOR)

Fig. 12. Hydraulic heads and boundary conditions of Ecca Aquifer. (COLOR)

Fig. 13. Schematic diagrams of: a) hydrogeological conceptual model of the Central Kalahari

Basin; b) numerical model schematisation. (COLOR)

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• Systematic data integration proposed in hydrogeological conceptual model development.

• 3D geological modelling tool vital in developing hydrogeological conceptual models.

• Independent 3D geological modelling codes preferred in developing conceptual model.

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