Published January 8, 2015
Journal of Environmental Quality
Long-Term Agroecosystem Research in the Central Mississippi River
Basin: Hydrogeologic Controls and Crop Management Influence on
Nitrates in Loess and Fractured Glacial Till
Newell R. Kitchen,* Paul E. Blanchard, and Robert N. Lerch
Abstract
Nitrogen from agriculture is known to be a primary source of
groundwater NO3–N. Research was conducted in a northeastern
Missouri watershed to assess the impact of cropping systems
on NO3–N for a loess and fractured glacial till aquifer underlying
claypan soils. Three cropped fields with 10 yr of similar
management were each instrumented with 20 to 25 monitoring
wells, 3 to 15 m in depth, in 1991 to 1992. Wells were sampled and
analyzed for NO3–N at least annually from 1991 to 2004. Initial
NO3–N concentrations were variable, ranging from undetectable
to >24 mg L−1 but averaged 7.0 mg L−1. Groundwater NO3–N was
significantly higher in Field 3, probably the result of concurrent
applications of manure and N fertilizer before 1980. Overall
changes in NO3–N levels in Fields 1 and 2 were generally small;
however, NO3–N levels for Field 3 have decreased an average of
0.28 mg L−1 yr−1. Excessive loading of N into the matrix of the glacial
till may have had a long-term impact on NO3–N for this field.
Despite the presence of dissolved O2 in the aquifer, evidence of
denitrification in some upper-landscape groundwater wells was
found. The greatest decreases in NO3–N concentration occurred
as groundwater moved through an in-field tree line or through
a riparian zone. While overall conclusions were complicated by
the long-term impact of past management, the capacity of the
till to buffer changes, hydrogeologic variability found among
wells, and the activity of biological processes, we conclude that
cropping practices during this study did not increase glacial till
NO3–N.
Copyright © American Society of Agronomy, Crop Science Society of America,
and Soil Science Society of America. 5585 Guilford Rd., Madison, WI 53711 USA.
All rights reserved. No part of this periodical may be reproduced or transmitted
in any form or by any means, electronic or mechanical, including photocopying,
recording, or any information storage and retrieval system, without permission in
writing from the publisher.
J. Environ. Qual. 44:58–70 (2015)
doi:10.2134/jeq2014.09.0405
Freely available online through the author-supported open-access option.
Received 30 Sept. 2014.
Accepted 20 Oct. 2014.
*Corresponding author (Newell.Kitchen@ars.usda.gov).
58
SPECIAL SECTION
LTAR IN THE CENTRAL MISSISSIPPI RIVER BASIN
T he use of fertilizers and pesticides has increased agri-
cultural grain production to record levels in much of
the world, but contamination of water resources from
fertilizer use has caused widespread ecological impairment and
economic costs to society for clean drinking water (State-EPA
Nutrient Innovations Task Group, 2009; Ribaudo et al., 2011).
Nitrogen fertilizer is, by mass, the single greatest agrichemi-
cal input on cereal grain crops. Production is tremendously
enhanced with N fertilization, with yield increases commonly
two to four times greater than without fertilization, and N addi-
tions are thus a critical input to help reach global food security
goals (Tilman et al., 2002). A negative consequence of N fertil-
izer use is hydrologic transport from farmland. One loss pathway
of concern is NO3− leaching below the root zone and into aqui-
fers. Nitrogen from synthetic fertilizers continues to be consid-
ered a primary source of elevated NO3–N in groundwater.
Nitrate is relatively nontoxic to humans and animals;
however, it can be reduced to NO2–N by denitrifying bacteria
in the upper digestive tract. High concentrations of NO2–N
can be toxic to humans, causing a serious blood disorder called
infantile methemoglobinemia or cyanosis (Manassaram et al.,
2006). Although the disorder is easily treated, in extreme cases
it can cause death. The reaction of NO2–N with the hemoglobin
of the blood reduces the capability of the blood to carry O2 to
the body tissues. Prompt medical attention normally results in
quick recovery (Zaporozec, 1983). A few cases of the disease
have been associated with foods high in NO3–N or NO2–N, but
nearly all cases reported in the United States have resulted from
the ingestion of NO3–N in private well water used to prepare
infant formula (Walton, 1951; Knobeloch et al., 2000). The risk
of methemoglobinemia increases measurably as concentrations
increase above 10 mg L−1 NO3–N. Recent studies on human
NO3 ingestion are mixed, but some have also shown increased
risk for digestive track or endocrine cancers (Ward et al., 2005,
N.R. Kitchen and R.N. Lerch, USDA–ARS Cropping Systems and Water Quality
Research Unit, 269 Agricultural Engineering Building, Univ. of Missouri, Columbia,
MO 65211; P.E. Blanchard, Missouri Dep. of Conservation, Conservation Research
Center, 3500 East Gans Road, Columbia, MO 65201. Assigned to Associate Editor
Mark Tomer.
Abbreviations: CMRB, Central Mississippi River Basin; DO, dissolved oxygen; GCEW,
Goodwater Creek Experimental Watershed; LTAR, Long-Term Agroecosystem
Research; MCL, maximum contaminant level; MSEA, Management Systems
Evaluation Area.
2010; Johnson et al., 2010; Kilfoy et al., 2011).While the 10 field sites (Fig. 1), and 25 wells were distributed throughout
mg L−1 NO3–N standard has been questioned using modern the watershed. Details of the well locations, depth below the
techniques of epidemiology (Avery, 1999), it still stands as the ground surface, and sampling frequency were reported by
maximum contaminant level (MCL) by the USEPA. Lerch et al. (2015). Descriptions of the geophysical setting,
National surveys (USEPA, 1990; Mueller et al., 1995), historic land uses and anthropogenic activities, and weather
national syntheses of local and regional surveys and studies data were provided as part of the data documentation for the
(Madison and Brunett, 1985; Fedkiw, 1991; Spalding and GCEW (Sadler et al., 2015). The data have served to develop
Exner, 1993; Burow et al., 2010), regional surveys (Burkart our understanding of the hydrogeology, the spatial and temporal
and Kolpin, 1993; Richards et al., 1996; Centers for Disease variation in contamination, and the effects of landscape features
Control and Prevention, 1998; Gormly and Spalding, 1979), on the fate of NO3–N for a shallow glacial aquifer underlying
and numerous state and local studies have investigated the extent claypan soils. In addition, it provides an example of the insights
of and factors related to NO3–N contamination of groundwater. that can be gained through the long-term and comprehensive
The percentage of wells with NO3–N exceeding the MCL varies development of the data sets collected within the GCEW. The
from study to study depending on the biases inherent in the data specific objectives of this research were to provide a detailed
sets, such as whether a study focused on public water supply or understanding of the hydrogeologic controls on NO3–N
domestic wells, agricultural or urban settings, or was dominated transport and the effects of three different cropping systems
by known or suspected problem areas. Numerous studies have on groundwater NO3–N concentrations within the GCEW
documented two primary factors in NO3–N contamination. from 1991 to 2004. The knowledge gained from this study has
The highest occurrence of wells in which NO3–N exceeds enhanced our understanding of the importance of vegetation
the MCL is when the screened interval of the wells is shallow and hydrogeologic controls on NO3–N contamination of
(defined differently in various studies, but generally less than streams within the region.
either 15 or 30 m) and/or when the wells are in agricultural
areas. Within agricultural areas, there are numerous sources of
N, all of which could contribute to NO3–N contamination.
These include levels of N fertilizer use, animal waste, septic
tanks, atmospheric deposition, and soil N. Contamination due
to N fertilizer could be from either point sources (e.g., spills or
back-siphoning of chemigation water) or nonpoint source from
normal fertilizer use. Contamination due to animal waste could
be from either point sources or nonpoint source from manure
use on fields. Important well characteristics include such factors
as the age, depth, diameter, and construction method (dug,
driven, or drilled) of the well and the proximity of the well to
cropland, chemical mixing sites, septic systems, or livestock areas.
These various factors are not mutually exclusive. For example,
Richards et al. (1996) noted that older wells are more likely to be
dug rather than drilled and that dug wells are likely to be shallow.
The hydrogeologic setting imposes additional factors affecting
the vulnerability of groundwater to NO3–N contamination.
These factors include soil texture, which controls infiltration
and percolation rates, aquifer type and depth, precipitation,
geochemical attenuation processes within the soil and aquifer,
and surface topography (Nolan and Hitt, 2006; Liao et al.,
2012). Land uses and land management practices that affect
the nature and extent of N inputs are then imposed on the
hydrogeologic setting. The existence of multiple factors and
complex interactions between the geophysical setting and
anthropogenic activities confounds the ability to isolate the
impact of any single factor. Thus, determining the impact of
nonpoint-source N fertilizer on groundwater quality requires
a detailed understanding of the hydrogeology and land uses
impacting an aquifer.
To better understand the combined effects of hydrogeology
and crop management effects, a long-term groundwater NO3–N
data set was generated within the Goodwater Creek Experimental
Watershed (GCEW) (Lerch et al., 2015). Beginning in 1991, a
network of 97 wells installed within the glacial till aquifer of the
Fig. 1. The 7250-ha Goodwater Creek Experimental Watershed in
GCEW was monitored for NO3–N concentrations. Seventy- north-central Missouri. A scaled-up version of this watershed location
two of the wells were adjacent to or within three research can be found in Sadler et al (2015).
www.agronomy.org • www.crops.org • www.soils.org 59
Materials and Methods
Site Description
The study site is the 7250-ha GCEW in north-central
Missouri (Fig. 1). The GCEW is near the southern terminus of
glaciation in the Dissected Till Plains physiographic province,
which includes significant portions of Kansas, Nebraska, Iowa,
and Missouri. This watershed is typical of the 2.8 million ha
Central Claypan region of Missouri and Illinois (NRCS, 1981).
This region is typified by the presence of a claypan, a naturally
occurring argillic soil horizon (clay content 450–650 g kg−1) that
typically occurs at a depth of 10 to 40 cm, depending on erosion
exposure.
Quaternary stratigraphic relationships for north-central
Missouri (Guccione, 1983; Sharp, 1984) were adapted for the
watershed based on core samples collected during this study
(Fig. 2). Two pre-Illinoian till units (200,000–750,000 yr;
Rovey and Balco, 2011) separated by a paleosol were found
at most locations. Erosion has removed the upper or lower till
units at some locations. A paleosol was also present at the top of
the glacial till which has been mantled by Illinoian (300,000–
120,000 yr) and Wisconsinan (100,000–25,000 yr) loess. The
area has since been subject to considerable weathering and
stream dissection. The loess and till decrease in thickness from
summit positions to lower landscape positions near the creek.
The loess can be >3 m thick and overlies as much as 15 m of till.
The till overlies Pennsylvanian age deposits of shale, limestone,
and clay, and in some locations pre-glacial sediments include
Fig. 2. A general representation of the stratigraphic relationships
of loess and glacial till layers originally described for north-central
Missouri (Guccione, 1983) but modified for the Goodwater Creek
Watershed based on drill core samples collected during this study.
Hydraulic conductivity was obtained from wells of this study as
previously reported (Blanchard and Donald, 1997). Hydraulic tests
of the upper and lower tills and the two paleosols were averaged for
representing those respective layers.
60 Journal of Environmental Quality
peat. Alluvial deposits are present near the creeks. Near the
outlet of the GCEW, the loess, till, and Pennsylvanian deposits
have been completely eroded and alluvium directly overlies the
Mississippian age Burlington Limestone. The loess and glacial
till have sufficient permeability and yield for domestic use
(Blanchard and Donald, 1997) and are referred to here as the
glacial aquifer.
The predominant soils including the Putnam (Mollic
Albaqualfs), Mexico (Udollic Ochraqualfs), Adco (Albaquic
Hapludalfs), and Leonard (Vertic Ochraqualfs) series developed
on the Wisconsin loess (NRCS, 1995). The claypan formed in
the loess by the accumulation of clay in the illuvial B horizon.
The low permeability of the claypan restricts percolation and
promotes the development of interflow and surface runoff
(Sharp, 1984). Additional details on the glacial material and soil
morphology of the GCEW landscape were provided by Sadler
et al. (2015).
The USDA–ARS has maintained climate and surface
hydrology instrumentation on the watershed since 1970. During
a 43-yr period (1970–2012), the average annual precipitation has
been 98.1 cm. Average annual stream flow exiting the watershed
(1992–2010) is 28.7 cm, with surface runoff accounting for
?85% of the total stream flow. Groundwater recharge has
previously been documented to occur primarily between the
months of November and May (Blanchard and Donald, 1997).
Other details of the GCEW ground and surface hydrology were
provided by Sadler et al. (2015).
Three farm fields (Fig. 1 and 3) approximately 2.5 km apart
from each other were selected in fall 1990 for assessing the
impact of cropping systems on ground and surface water quality.
The fields were chosen because they have soils typical of the
Central Claypan region, were located at topographic divides,
were suitable for ground and surface water monitoring, and
had been managed similarly the decade before initiating this
research. Farming practices and evaluation associated with the
Management Systems Evaluation Area (MSEA) project began
on the fields in 1991. Annual N fertilizer rates along with the
crop rotation sequence for the three field cropping systems were
typical for the region and are provided in Table 1. Tracking of N
inputs and other crop management details ceased at the end of
the 2001 growing session for Fields 2 and 3.
Well Drilling and Construction
Groundwater wells were drilled in the spring of 1991, before
the implementation of the prescribed farming systems. Each field
was instrumented with five well nests, with three to four wells
in each nest (Fig. 3). At least three nests per field were located
within the field boundary, with the additional nests positioned
along the field edge. The wells within each nest were within close
proximity of each other, with the total nest area encompassing
about 25 m2. No agrichemicals were applied to the well nest
area. The 5.08-cm-diameter polyvinyl chloride (PVC) wells were
installed through 16.5-cm-diameter hollow-stem augers. The
borehole annulus was backfilled with sand to 30 cm above the
well screen, followed by 2 m of bentonite and, from the top of the
bentonite to the land surface, with a cement–bentonite grout.
These initial wells had 1.2-m-long slotted PVC screens. The wells
in each nest were screened at different depths to determine water
quality differences with depth. The deepest well in each nest was
Fig. 3. Field boundaries and elevation for the three fields intensively monitored for groundwater nitrates. Letters show well nest locations.

Table 1. Nitrogen input and cropping history of fields.

Applied N Cropping history†
Year
Field 1 Field 2 Field 3 Field 1 Field 2 Field 3
—————————— kg ha−1 ——————————
1991 190 101 118 corn sorghum corn
1992 0 0 0 soybean soybean soybean
1993 190 101 84 corn sorghum wheat
1994 0 0 151 soybean soybean corn
1995 110 101 0 sorghum sorghum soybean
1996 0 0 84 soybean soybean wheat
1997 190 151 151 corn corn corn
1998 0 0 0 soybean soybean soybean
1999 190 151 151 corn corn corn
2000 0 0 0 soybean soybean soybean
2001 190 144 151 corn corn corn
2002 0 NA‡ NA soybean NA NA
2003 190 NA NA corn NA NA
Assessment annual mean§ 96 68 81
Assessment total§ 1250 749 890
† Nitrogen fertilization occurred in late February or March for wheat and April or May for corn and sorghum.
‡ NA, not available.
§ Mean and total are 13 yr for Field 1 and 11 yr for Fields 2 and 3.

www.agronomy.org • www.crops.org • www.soils.org 61

screened at the bottom of the till, except for the deepest wells in
nests 3B, 3C, and 3E, which were screened in preglacial peat just
below the till (Fig. 2). The screened intervals of the succeeding
shallower wells in each nest were chosen to correspond with
fractures, sand lenses, and color changes observed in continuous
cores collected during well drilling. In 1992, 10 additional wells
were installed, one at each nest where the water table was higher
than the shallowest well installed in 1991. These 10 wells were in
the loess and have 0.6-m slotted PVC screens. Thus, for the three
fields, a total of 72 monitoring wells were installed. Elsewhere, 18
additional glacial aquifer wells at depths from 3 to 10 m and five
alluvial wells at depths from 2 to 8 m were drilled in 1990 within
the surrounding GCEW (Fig. 1). Two extra shallow wells were
installed in 1992 along a riparian corridor bordering the west
side of Field 3.
Core Collection and Analysis
A continuous core sample was collected during the drilling
of the deepest well at each well nest. The samples were collected
with a 1.6-m-long, 7.62-cm-diameter core barrel that had a
removable acetate liner. The core barrel advanced ahead of the
augers and was mounted on a bearing to prevent rotation of the
core barrel. The core barrel was retrieved every 1.6 m, and the
liner was removed, capped, numbered, and placed in a cooler.
The core samples were brought to the laboratory at the end of
the day and refrigerated.
In the laboratory, the core samples were divided horizontally
according to soil horizons or visible textural or color changes.
Where the core appeared uniform, it was divided into 30-cm
increments. The core segments were divided longitudinally
twice. One quarter of each sample was sent to the USDA Soil
Tilth Laboratory (now the USDA National Laboratory for
Agriculture and the Environment) for NH4–N and NO3–N
analysis. Soil NH4–N and NO3–N were extracted with 2 mol
L−1 KCl (Keeney and Nelson, 1982). Nitrate was measured
colorimetrically by reduction to NO2–N using a Cd column
and a continuous-flow autoanalyzer (Lachat Instruments). The
detection limit for this method was 0.5 mg N kg−1 dry soil. A
second quarter of each sample was sent to the University of
Missouri-Columbia Soil Characterization Laboratory for
analysis following accepted methods (Soil Survey Laboratory
Staff, 1996) including particle size (pipette method), cation
exchange capacity and exchangeable cations (1 mol L−1 NH4OAc
extractable at pH 7.0), saturated paste pH, and organic C content
(dry combustion).
Well Tests, Sampling, and Analysis
Hydraulic conductivity (K) was measured on wells in
1992. For most wells, a falling-head slug test using a water-
tight 2.54- by 1.52-cm PVC displacement cylinder provided
reproducible results. For some wells, this procedure produced
no appreciable response and a rising-head after-pumping test was
used. Models suitable for unconfined aquifers were considered
when calculating K, with additional details documented by
Heidenreich and Blanchard (1993).
Wells were sampled quarterly from March 1991 to March
1996 and semiannually from March 1996 through 2004. Not
all wells were sampled each quarter because some wells were dry
at the scheduled time of sampling, but in at least one quarter
62 Journal of Environmental Quality
each year every well was sampled. Sampling was discontinued
at the end of 2001 for Field 2. Each well was equipped with a
dedicated WaTerra (WaTerra Pumps, Ltd.) hand pump. The hand
pump was composed of 1.59-cm (0.625-in) o.d. high-density
polyethylene tubing with a Delrin (DuPont, Inc.) plastic foot
valve. Three well volumes of water were purged from each well
before sample collection. Samples were collected in 900-mL
amber glass bottles, placed in a cooler, and transported to the
laboratory at the end of the day.
Chemical Analyses
Water samples for NO3–N analyses were filtered within 48
h of sampling through 0.45-mm nylon syringe filters to remove
suspended sediment. From 1991 to 1993, samples were preserved
before analysis by H2SO4 treatment to a pH of approximately 2
and refrigerated (Lerch et al., 2015). Analysis for NO3–N was
done within 28 d. Beginning in 1993, samples were filtered,
refrigerated, and normally analyzed within 5 d of collection. If
samples could not be analyzed within 5 d, they were frozen and
analysis was done within 30 d of collection. The Cd reduction
method was used to determine NO3–N concentrations using
different instrumentation over time as described by Lerch et al.
(2015). The detection limit for the analyses was 0.05 to 0.10 mg
L−1 NO3–N. Initially, separate analyses of NO2–N and NO3–N
+ NO2–N were conducted. Nitrite proved to be insignificant
relative to NO3–N and the separate NO2–N analyses were
discontinued after 1992. We refer to (NO3 + NO2)-N results as
NO3–N.
Dissolved O2 (DO) measurements were conducted using a
Hydrolab H20G multiprobe (Hydrolab Corp.), which allows
simultaneous in situ logging of pH, specific conductance, DO,
and oxidation–reduction potential. After calibration, the probe
was deployed in the well so that the sensors were at the level of
the well screen. One well volume of water was purged from the
well before datalogging. To maintain flow past the sensors, the
well was pumped while continuously measuring the parameters.
The test was considered complete when all parameters remained
steady for 3 min.
Statistical Analyses
Descriptive statistics of NO3–N concentrations were
obtained by field and well nest, and were related to other well
properties to explore potential meaningful relationships of
management to hydrologic properties of the GCEW. Trends in
NO3–N concentration changes within each well during the 13-yr
period (11 yr for Field 2) were statistically tested by comparing
the first half of the assessment time with the second half using a
Wilcoxon–Mann–Whitney ranked sums test (Helsel and Hirsch,
2002). Wells found to be different using this test (a = 0.05) were
then further tested using simple linear regression with decimal
year as the independent variable, adjusted for autocorrelation
when the Durbin–Watson statistic was significant (a = 0.05).
Slopes of the regressions were used to represent when significant
changes had occurred (F test a = 0.05; Ho: linear slope during
assessment period = 0).
Results and Discussion
Hydrogeology of the Study Site
Nitrate transport by groundwater cannot be evaluated
without an understanding of the hydrogeology of the site. The
hydrogeology of the study site and its influence on the transport
of herbicides and herbicide metabolites was discussed in detail by
Blanchard and Donald (1997). A brief summary is provided here
to aid in the interpretation of NO3− transport processes. The
glacial aquifer hydrology is complex; it behaves in most locations
as a water table aquifer, but in other locations the paleosols or
preglacial clays act as leaky confining units. Sharp (1984) noted
that field-measured hydraulic conductivities of pre-Illinoian till
in Missouri are two to four orders of magnitude higher than
those determined on small laboratory samples. The hydraulic
conductivity tests conducted on the study wells (Heidenreich
and Blanchard, 1993) were consistent with that finding and are
summarized in Fig. 2. The low topographic slope of the GCEW
is reflected in the hydraulic gradients in the study area, which
are in the range of 0.005 to 0.02. Transport of mobile herbicide
metabolites through the aquifer was rapid, especially at Fields 2
and 3 (Blanchard and Donald, 1997). Rapid transport in this
system is consistent with preferential flow through fractured
till. Blanchard and Donald (1997) concluded that the upper
till paleosol is hydrologically the limiting unit for transport of
dissolved chemicals that have reached the water table.
Time Zero Nitrate
Initial groundwater samples were collected in spring and
early summer of 1991 as the project farming systems were being
implemented on the farm fields. Nitrate concentrations in these
three field baseline samples were quite variable, ranging from
undetectable to >24 mg L−1 (Fig. 4). The median and mean
NO3–N concentrations were 5.0 and 7.0 mg L−1, respectively,
with 24% of the samples exceeding the MCL. From these baseline
samples, the highest concentrations for each field occurred at
the 6- to11-m well depth (Fig. 5), with concentrations generally
lower above and below. However, due to the wide variance in
NO3–N concentration with depth, statistical significance of
concentration as a function of well depth was weak for each field
Fig. 4. Groundwater NO3–N concentrations shown for initial (1991 all fields) and final (2004 for Fields 1 and 3, 2001 for Field 2) samplings. Results
exclude shallow wells drilled in 1992. Values from the field wells are contrasted with values obtained from 18 watershed wells.
www.agronomy.org • www.crops.org • www.soils.org 63
(best-fit quadratic or cubic model R2 values of 0.28, 0.19, and
0.36 for Fields 1–3, respectively).
All the wells in this study were <15 m deep and would have
been classed as shallow wells in the national and regional surveys.
The initial median and mean for surrounding GCEW well
NO3–N concentrations were 1.6 and 5.2 mg L−1, respectively,
with 28% of the samples above the MCL. Taken as a whole, the
NO3–N in wells from the three fields was statistically similar to
that of the wells in the surrounding watershed (Fig. 4), although
some wells from Field 3 were identified as outliers when field
results were combined. On a field-by-field basis, NO3–N results
from Field 3 were significantly different from Fields 1 and 2. A
plot of NO3–N in the initial well samples vs. NO3–N in the
corresponding core samples (Fig. 6) shows that Fields 1 and
2 were similar overall, but many of the Field 3 well and core
samples were higher in NO3–N than those of Fields 1 and 2.
The well samples represent water from fractures, while the core
samples represent an estimate of the matrix NO3–N.
Because these three fields had been managed in a similar
manner in the 10 yr before this research began, no major
differences in groundwater quality had been anticipated. Field
history records and interviews with landowners and farm
managers were used to create a timeline of management history
(i.e., crops, rotations, N fertilizer management, and manure
management) of the three fields from 1930 to 1990 (Kitchen et
al., 1997). From 1930 to 1980, Field 3 had apparently received a
greater total N application than the other two fields. Corn was
grown more often in the 1970s on this field, and between 1930
and 1981, manure was spread from nearby (but hydrologically
separate) livestock feeding areas. Livestock animals were also
occasionally overwintered on Field 3.
Impact of Cropping Systems on Nitrate
As noted, a primary goal of the Missouri MSEA was to assess
the water quality impacts of typical cropping systems within
the GCEW. For the 6 yr before this study (1985–1990), N
fertilizer input was accounted for from farmer records and the
average annual N input was 34, 67, and 45 kg ha−1 for Fields 1,
2, and 3, respectively. Crop rotations and associated N fertilizer
management for the farming systems of this study are presented
 Table 2. Annual mean NO3–N of field wells averaged from the first and
third quarter of each year (when sampled).
Mean NO3–N
Year
Field 1 Field 2 Field 3
———————— mg L−1 ————————
1991 4.2 4.8 12.4
1992 4.5 4.4 10.7
1993 5.1 4.7 10.6
1994 4.7 4.4 9.2
1995 4.9 4.2 9.5
1996 4.8 4.3 9.6
1997 5.0 4.2 9.3
1998 4.7 4.1 8.7
1999 4.7 4.2 7.9
2000 4.7 4.4 7.7
2001 4.3 4.4 8.0
Fig. 5. Nitrate-N concentrations as a function of well depth for each 2002 5.7 9.0
of the three field sites. Depth of wells was not an important factor
2003 5.1 8.0
explaining NO3–N levels. These results were from the initial samples
from the three fields. 2004† 4.8 8.9
† First quarter only.

Nitrate-N concentration by field, nest, and each individual

Fig. 6. Relationship between initial NO3–N concentrations in
groundwater (detection limit <0.01 mg L−1) and corresponding
sediment core (detection limit = 0.5 mg kg−1) samples.
in Table 1. Thus with the initiation of the research, N inputs on
Field 2 were similar to pre-investigation years and Fields 1 and 3
represented increased N fertilization.
Nitrate-N concentrations of the initial field and watershed
samples are summarized and compared with the final samples
taken 11 or 13 yr later (Fig. 4). The annual average NO3–N
concentration is also summarized by field during the 13 yr (Table
2). Combined across fields, the final median and mean NO3–N
concentrations were 5.2 and 6.1 mg L−1, respectively. For the
watershed, final median and mean NO3–N concentrations
were 4.0 and 6.7 mg L−1, respectively. While the final mean
values are slightly lower than the initial samples for the fields
and slightly higher for the watershed, at this aggregate level no
significant difference using the Wilcoxon rank sum test was
found between the beginning and the end samplings. The 90th
percentile of NO3–N concentrations in the watershed wells has
increased dramatically due to three wells that have increased by
8 to 10 mg L−1. The N input in the vicinity of these wells was
unknown, although we suspect that irrigation management of a
nearby pivot system (not common in the watershed) was a factor.
well are shown for the period of this assessment (Fig. 7). On
each field, some wells appear to have decreased with time, some
increased, and some have remained nearly invariant in NO3–N.
For many wells, NO3–N changes have been small and gradual,
but a few wells have shown significant temporal fluctuations
(discussed below). Seasonal or crop-rotational trends in NO3–N
concentration were not present or were not obvious.
Nitrate concentration during the 13-yr assessment period was
statistically evaluated to determine where changes have occurred
(Fig. 8). Average annual NO3–N change rates are shown relative
to the initial well NO3–N concentrations. Some wells from all
three fields statistically increased in NO3–N concentration (five,
nine, and two wells for Fields 1, 2, and 3, respectively), although
no wells showed an average annual increase of >0.35 mg L−1 yr−1.
An initial concentration <12 mg L−1 seemed to have no bearing
on whether NO3–N levels increased. Wells showing significant
increases averaged only 0.16, 0.17, and 0.15 mg L−1 yr−1 for Fields
1 to 3, respectively. Likewise, all three fields had some wells that
significantly decreased in NO3–N (three, nine, and nine wells
for Fields 1, 2, and 3, respectively). By far, decreases were most
prominent from Field 3, with the average of wells showing
decreases being 0.70 mg L−1 yr−1 compared with 0.44 mg L−1 yr−1
for Field 1 and 0.23 mg L−1 yr−1 for Field 2. In some cases, all
wells within a nest changed similarly. For example, all wells in
Nest 2B significantly increased and all wells in Nests 2C and 2D
decreased. However, one third of field well nests had at least one
well that increased and one that decreased, suggesting multiple
processes at work controlling NO3–N transport and storage
within these fields.
The decrease in NO3–N concentrations from Field 3 was
especially notable in the up-gradient well nests (3A and 3B),
which had the highest concentrations in 1991. This decrease
reflects the influence of both the pre-1990 management and the
management during this assessment period. Judging by the long-
term impact of management shown by the pre-study samples at
Field 3, it was difficult to make definitive statements regarding
the impact of the prescribed cropping systems even after the

64 Journal of Environmental Quality

Fig. 7. Quarterly groundwater NO3–N concentrations shown by field, nest, and individual well during this investigation period. Note that well depth
in meters is provided on the nest legend.

www.agronomy.org • www.crops.org • www.soils.org 65

decade plus of monitoring represented by this investigation. were 5 to 15 mg L−1 higher in 1980 than they were for the initial
Nevertheless, some statements can be made based on the data. sampling in 1991.
Field 1 which had the highest N input, showed a slight
upward trend in mean NO3–N concentrations (Table 2). Hydrogeologic Controls and Impact on Nitrates
However, averaging among individual wells as shown in Fig. 8 Differences among the fields were mainly attributed to the
(increasing, decreasing, and no change), the rate of change has variable hydrogeologic controls that impact NO3–N transport
been minor (−0.003 mg L−1 yr−1). This slight decrease suggests in the glacial aquifer. These controls vary in depth from the
that minimal NO3–N is transported through the loess and upper surface to the preglacial deposits and include both physical and
till paleosol, making it extremely difficult to assess the impact of biochemical controls (Liao et al., 2012). While the low hydraulic
subtle differences in cropping system N fertilizer inputs. This is conductivity of the claypan significantly limits recharge, site-
supported by measurements that show that of the three fields, specific preferential flow through the subsoil and till material can
the groundwater system at Field 1 is the slowest hydrologically dominate over matrix flow, as has been well described previously
as a result of a lower hydraulic gradient and the influence of a for this research site (Blevins et al., 1996; Blanchard and Donald,
thicker and/or less permeable upper till paleosol (discussed 1997; Kitchen et al., 1998; Wilkison and Blevins, 1999; Pagan,
below). An additional indication that the Field 1 farming system 2009). For this investigation, other relationships were examined
had not yet affected the majority of Field 1 wells is the fact that to try to better understand hydraulic control within the till.
fewer herbicides and herbicide metabolites have been detected Hydraulic conductivity (K) as a function of well depth showed
at Field 1 than at Fields 2 and 3, even though Field 1 had the no meaningful relationship because both shallow and deeper
highest herbicide application rates (Blanchard and Donald, wells exhibited low and high K (Fig. 9). Hydraulic conductivity
1997). More recent results showed that atrazine [6-chloro- trended lower with higher clay content in the till of the fields,
N-ethyl-N¢-(1-methylethyl)-1,3,5-triazine-2,4-diamine] and but this relationship was weak (R2 = 0.21, 0.19, and 0.07 for
metabolite concentrations at Field 1 have increased with time, Fields 1–3, respectively; Fig. 10). When we examined the
but the concentrations were still very low because of the low initial sampled NO3–N concentration (Fig. 11) or variation in
hydraulic conductivity of the claypan (Pagan, 2009).
Field 2, which is most similar to pre-study N management,
showed a small decrease in the mean NO3–N values. Averaging
across all wells, the rate of decrease was only 0.03 mg NO3–N
L−1 yr−1.
Field 3 showed a major decrease in NO3–N concentrations,
especially in the up-gradient well nests (3A and 3B in Fig. 7).
The decrease for all wells averaged 0.31 mg L−1 yr−1. This decrease
reflects both the influence of excessive N loading with concurrent
N fertilizer and manure applications before 1980 (Kitchen et al.,
1997) and the modest N application since then (average 68 kg
N yr−1 for 1985–2001). A quantitative record of N applications
before 1985 is unavailable, and thus the impact of concurrent N
fertilizer and animal manures before 1980 on aquifer loading is
uncertain. If available, such records would allow quantification
of the lag effect of inputs on groundwater NO3–N for this
hydrologic setting. If the lag times were no more than a few years, Fig. 9. Hydraulic conductivity (K) of wells in this investigation was not
we could conservatively estimate, using the regression results for a function of well depth.
wells decreasing in NO3–N concentrations, that these same wells

Fig. 8. Trends in NO3–N concentration during the 13-yr assessment

period (11 yr for Field 2) for the first- and third-quarter samples. Wells Fig. 10. Hydraulic conductivity (K) of wells in this investigation was
with significant change are shown as points off the zero-slope line. weakly related to total clay in the matrix.

66 Journal of Environmental Quality

NO3–N concentration during the assessment period (measured
by standard deviation in NO3–N; results not shown), no clear
pattern was observed. These various tests on K, along with the
weak relationship between NO3–N and well depth (Fig. 5),
support the dominance of a preferential flow system. Although
all three fields are located at surface water divides, Field 1 is at
the primary divide between the GCEW and the adjacent Youngs
Creek Watershed, while Fields 2 and 3 are located at secondary
divides within the GCEW (Hesemann, 1979). The divide at
Field 1 is characterized by flat topography and a low hydraulic
gradient. No data are available to indicate that recharge through
the claypan varied among these fields. The most important
constraint on flow in the glacial aquifer may be the upper till
paleosol, which limits flow and transport from the loess to the
more permeable till (Fig. 2). The combination of the lower
gradient and the less transmissive upper till paleosol reduced the
rate of solute transport at Field 1 relative to Fields 2 and 3 and
was previously documented by Blanchard and Donald (1997)
for these same fields.
Taking into account both the history of past management from
these fields and the hydrogeologic assessment from the wells, a
mechanism was needed to explain the initially high NO3–N levels
found at Field 3. Matrix diffusion of NO3–N between the mobile
water in the fracture and the immobile water of the matrix was
a probable mechanism for at least some of the wells (Grisak and
Pickens, 1980; Grisak et al., 1980). The high pre-study NO3–N
found in Field 3 was probably the result of higher N inputs before
1980. Dissolved O2 measurements made in the glacial till wells
were in the 2.5 to 8 mg L−1 range, which indicated that NO3–N
was stable in the fractures (Gillham and Cherry, 1978). High
DO in the fractures not only precluded denitrification within
the fracture but also provided DO to the matrix by diffusion and
thus limited denitrification in the matrix. If high concentrations
of NO3–N were present in the fractures for a long period of time
(before 1980), then a large amount of NO3–N could be stored in
the aquifer due to diffusion from the fractures to the matrix. More
conservative N management at the land surface may have reduced
the NO3–N concentration in the water recharging the aquifer, but
the NO3–N stored in the matrix could diffuse back to the mobile
water and thus keep NO3–N concentrations in the mobile water
high. Over time, the stored matrix NO3–N would diminish, and
thus eventually the mobile water NO3–N concentrations would
also decline. Declining NO3–N concentrations from 1991 to
2004 fit this mechanism. Figure 6 shows that the wells with the
highest NO3–N in the water also had the highest NO3–N in
the corresponding core samples. These wells were located at two
summit positions within Field 3 (Nests 3A and 3B in Fig. 3) and
were representative of the recharge zone of the aquifer. There
were some wells (Fig. 6) that had significant concentrations of
NO3–N in the water but little or undetectable NO3–N in the
corresponding core samples. It is unknown if insufficient time
has passed to allow large amounts of NO3–N to diffuse into the
matrix or if these were locations where denitrifying conditions
existed within the matrix. This fate and transport description is
consistent with all known data from the site.
A dramatic example of the hydrogeochemical complexity of
NO3–N transport in the till and preglacial deposits was found
at Nest 3B, which is located at a summit position within Field 3.
Well 3B1 (14.0-m depth) is screened in preglacial peat below the
www.agronomy.org • www.crops.org • www.soils.org 67
Fig. 11. Initial NO3–N concentrations as a function of hydraulic
conductivity (K) of wells.
till, 3B2 (11.7-m depth) is screened near the base of the lower
till, and 3B4 (8.1-m depth) is screened in the upper till. We
hypothesized that this high organic C zone would be conducive
to denitrification (Puckett, 2004). Major fluctuations (>8 mg
L−1) were noted in 3B1 and 3B2 during quarterly sampling in
1991 and 1993. During this time period, Well 3B4 showed a
dramatic decline in NO3–N concentration of approximately
10 mg L−1 (Fig. 7). The drill core samples from the depth range
of 3B2 and 3B4 were some of the highest of all the wells, with
NO3–N in the 2.5 to 3 mg kg−1 range. Therefore, long-term
storage of NO3–N had occurred in these parts of the aquifer.
To better understand the hydrogeologic processes occurring in
the aquifer, sampling for NO3–N and measurements of hydraulic
head were conducted weekly for these three wells from March
1994 to March 1995 (Fig. 12). Vertical hydraulic gradients were
due to the lower permeability of the lower till paleosol between
3B4 and 3B2 and by about 60 cm of preglacial clay between 3B2
and 3B1. Despite these zones of lower permeability, all wells in
this nest had detections of herbicide metabolites (Blanchard and
Donald, 1997), thus demonstrating that hydraulic connectivity
exists from the land surface to the base of the aquifer. The NO3–N
concentration in 3B1 (the peat well) was highly dependent on
the flux of NO3–N from above (3B2). When the head in 3B2
was higher than in 3B1, the rate of NO3–N transport into the
till apparently exceeded the rate of denitrification within the
peat. When the head difference between 3B2 and 3B1 declined,
the 3B1 NO3–N concentration declined. Between August
and November 1994, the head in 3B1 was higher than in 3B2.
Therefore the only NO3–N transport between the till and the
peat was by diffusion and the 3B1 NO3–N became undetectable.
During this time period, NO3–N in 3B2 declined from around
13 to 8 mg L−1. This decline can be explained as a combination
of advection of zero-NO3–N water from the peat into the till
and continued diffusion of NO3–N from the till into the peat.
From March to July 1994 and December 1994 to March 1995,
the NO3–N concentration in 3B2 had only relatively minor
fluctuations, similar to 3B4 for the entire year. These relatively
minor fluctuations were probably a combination of complicated
variations in advection and diffusion between the fractures and
the matrix. Quarterly samples from wells located in the peat
down-gradient from 3B1 had undetectable concentrations of

Fig. 12. Relationship between hydraulic gradient and changes in
NO3–N for three wells in Nest B of Field 3. The deepest well in this nest
(B1) was installed in preglacial peat.
NO3–N. Thus, the interaction of these variations in advective
transport with the chemical processes of diffusion and
denitrification was so complex that a single sample in time could
never represent the NO3–N contamination of the portion of the
aquifer sampled by Wells 3B1 and 3B2.
Riparian Zone Influence on Nitrates
Glacial aquifer water flow has been well characterized for this
study area, showing that the aquifer acts as a water table aquifer,
that flow within the aquifer is toward the creeks, and that as the
water table drops, the creek completely dries and there is no flow
(Hesemann, 1979; Blanchard and Donald, 1997). The glacial
aquifer within the watershed is not currently used as a significant
source of drinking water. However, the base flow of Goodwater
Creek, like many other streams within the Mississippi River
basin, is due to groundwater discharge. Base flow represents only
15% of the total stream flow of Goodwater Creek. However, that
base flow would represent a significant mass of N if it had the
average NO3–N concentration of the glacial aquifer wells (?7
mg L−1). In actuality, base-flow NO3–N concentrations in the
creek averaged only 0.59 mg L−1 from 1991 to 2004 (Baffaut et
al., 2009). There are several plausible reasons for the difference
in concentration. Some alluvial wells show seasonal changes in
NO3–N, with concentrations in March and June being less than
in September and December (Fig. 13). Nitrate values from some
68 Journal of Environmental Quality
Fig. 13. Groundwater NO3–N values from alluvial wells installed in the
riparian zone of Goodwater Creek and bordering along the west side
of Field 3.
wells changed by >5 mg L−1 in two successive quarters. This was
consistent with the process of N uptake by riparian vegetation,
which would probably be highly effective at NO3–N uptake
based on riparian width, vegetation type, and flow pathway
(Mayer et al., 2007). However, wells slightly deeper and more
associated with groundwater flow to stream base flow had greater
evidence of denitrification. One well (3G1) had no detectable
NO3–N for most of the monitoring period (Fig. 13). This same
well was known to give off a distinct odor of H2S, indicating that
the system was more reducing than necessary for denitrification.
While in-stream or riparian vegetation seemed to be
responsible for the removal of some NO3–N in the riparian
corridor, denitrification was probably more important in
changing concentration values as water moved into the base flow
of the stream. Average base-flow NO3–N in Goodwater Creek
was ?2 mg L−1 in January when vegetative utilization presumably
was at a minimum, while it was <1 mg L−1 in August when
vegetative usage would be high. This, along with the difference
in NO3–N concentration between upland glacial till and base
flow, suggested that the primary mode of NO3–N loss was by
denitrification within either the riparian zone or the streambed,
and that uptake by riparian or in-stream vegetation was of
secondary importance in this setting. Others have reported the
magnitude of denitrification in riparian areas to be about 4 to
20 times higher than vadose-zone denitrification rates found
upslope (Liao et al., 2012). Our findings of multiple processes
causing changes in NO3–N along a flow path through riparian
areas and into streams are consistent with summarized studies
(Puckett, 2004).
Tree Line Influence on Nitrates
In a non-riparian setting, deep-rooted trees within or on
the edges of fields may also alter shallow aquifer NO3–N
concentrations. An example was Nest 1B, located 20 m north
of an old fence row that today has overgrown with native shrubs
and trees 15 to 20 m in height. Because the groundwater flow
direction in this field is north to northwest (Pagan, 2009), these
wells are on the “downstream” side of this tree line. Nitrate-N
concentrations from wells in this nest have consistently been some
of the lowest for this field, averaging 1.5 mg L−1 compared with
6.9 mg L−1 for the nest “upstream” from the tree line (Fig. 7, 1A).
With a low hydraulic gradient in this field, shallow groundwater
flow through the tree line is slow, and this apparently facilitated
significant plant uptake of N. The tree line is relatively young.
There was little visual evidence of trees in this fence row in a 1939
aerial photo of the field. Images taken in the late 1950s indicate
small trees growing along the fence row, although a 1982 aerial
image shows many of the trees removed. Yet within a decade of
that photo, and at the time the groundwater wells were installed
on this field (1991), trees and large shrubs had been allowed to
return and remained during the time of groundwater monitoring.
During the study, the tree-line width was approximately 10 to
12 m, and growth into the field was controlled with tillage and
occasional root pruning.
Conclusions
The study provided a long-term investigation of the impact
of farming systems on groundwater quality. The use of within-
field, properly constructed monitoring wells eliminates many of
the complicating factors that have limited the interpretability of
water quality surveys. A number of important key points can be
made from this study.
There was no clear evidence that the farming practices used
during this investigation contributed to increased nonpoint-
source NO3–N groundwater contamination; however,
interpretation was complicated by the long-term impact of
past management, the capacity of the till to buffer changes in
NO3–N, the hydrogeologic variability found among well sites,
and the activity of biological processes. It was apparent that
for one field, significant contamination occurred due to prior
farming practices in which excess N loading from concurrent
applications of manure and fertilizer contributed to high
NO3–N in the groundwater. In this case, the long-term impact
has lasted more than 20 yr and current practices are resulting in
decreased contamination.
The majority of groundwater recharge for this setting is from
November to May. Therefore, minimizing the NO3–N in the
recharge water requires minimizing soil NO3–N during this
recharge period. Applying fertilizer N in accordance with best
management practices is considered essential for the protection
of groundwater quality.
Hydrogeologic processes controlling the transport of NO3–N
concentrations in groundwater resulted from a combination of
diffusion from the aquifer matrix and site-specific preferential
flow. Variation in the properties of the glacial aquifer (such as
the slope and thickness of the loess, tills, and paleosols) had a
profound impact on NO3–N transport. The dual-porosity
system of the till provides the opportunity for rapid solute
transport in the fractures, but matrix diffusion can buffer the
solute concentrations and thus retard transport. Changes in
till NO3–N concentrations with time were generally minor.
However, concentrations were temporally dynamic where
complexity was found in the till material, recharge and flow, and
historic NO3–N stored in the till matrix.
Hydrogeologic processes were modified by biological
processes such as plant uptake and denitrification. Our results
support denitrification as probably more important in NO3–N
reductions as groundwater flows from the till into stream
alluvium and into streams. Secondarily, riparian vegetation also
attributed to removal of NO3–N in stream base flow. Edge-of-
field trees also significantly reduced groundwater NO3–N.
www.agronomy.org • www.crops.org • www.soils.org 69
The results from this investigation within the GCEW
represent the broader Salt River Basin (6417 km2 or 2478
mi2) and establish an improved understanding of groundwater
hydrology for the Central Mississippi River Basin (CMRB)
site of the USDA-ARS Long-Term Agroecosystem Research
(LTAR) network. As such, this investigation provides a better
understanding of the interactions and complexities that
exist when combining the effects of spatially heterogeneous
hydrogeology, groundwater geochemistry, and crop
management. The treatment imposed at the initiation of this
work (e.g., cropping system) in the presence of this complexity
yielded few definitive answers. In the end, the data provoked
inquiry and additional sampling and measurements that
resulted in improved understanding of the hydrogeology
and the factors influencing spatial and temporal variation in
NO3–N contamination for this setting.
Acknowledgments
We wish to thank all the ARS and University of Missouri support staff
whose dedicated efforts have made this research investigation possible.
Special thanks to: Scott Drummond for assistance with data analysis
and graphics; Matt Volkmann, Richard Hamilton, and Mark Olson for
sample collection; Bettina Coggeshall, Jen Nelson, Dr. Lynn Stanley,
Joe Absheer, and Amber Spohn for laboratory analysis; and Teri Oster
and Michelle Pruitt for development and operation of the laboratory
information management system, data management, and quality
control.
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