Regular Article Journal of Geophysical Research: Oceans

DOI 10.1002/jgrc.20411

Suspended sediment transport in the Deepwater

Navigation Channel, Yangtze River Estuary, China in

the dry season 2009 - Part II: Numerical simulations

Dehai Song1, 2*, Xiao Hua Wang1, 2

1 Key Laboratory of Physical Oceanography, Ministry of Education, Qingdao

266003, P. R. China

2 School of Physical, Environmental and Mathematical Sciences, University of New

South Wales, Canberra, ACT 2600, Australia

*
Corresponding author

E-mail address: songdh@ouc.edu.cn

This article has been accepted for publication and undergone full peer review but has not been
through the copyediting, typesetting, pagination and proofreading process which may lead to
differences between this version and the Version of Record. Please cite this article as
doi: 10.1002/jgrc.20411

© 2013 American Geophysical Union

Received: Mar 23, 2013; Revised: Sep 15, 2013; Accepted: Sep 18, 2013
Abstract:

A three-dimensional wave-current-sediment coupled numerical model with wetting

and drying process is developed to understand hydrodynamics and sediment transport

dynamics in the Deepwater Navigation Channel (DNC), the North Passage of the

Yangtze River Estuary (YRE), China. The model results are in good agreement with

observed data, and statistics show good model skill scores and correlation coefficients.

The model well reproduces the spring-neap variation between a well-mixed estuary

and a highly-stratified estuary. Model results indicate that the estuarine gravitational

circulation plays the most important role in the estuarine turbidity maximum (ETM)

formation in the DNC. The upstream non-local sediment intrusion through the spill-

over-mechanism is a major source of sediment trapping in the North Passage after the

morphological changes. Numerical studies are conducted to show scenarios in the

YRE under the effects of different forcings (river-discharges, waves, and winds).

Between these study cases, surface-wave-breaking relieves the sediment trapping and

bottom-wave-current-interaction aggravates the bed erosion and elevates the SSC in

the ETM; the former and the latter have the least and largest influence on the

suspended sediment transport in the DNC. The wind effects have a greater influence

on sediment trapping than the river-discharges, and the steady-northwesterly-wind

condition favours the siltation in the DNC most. The significance of density-driven

turbidity current is also assessed, which can enhance the saline-water intrusion and

suppress the turbulent mixing in the bottom boundary layer.

Key words: Deepwater Navigation Channel; Yangtze River Estuary; suspended

sediment transport; estuarine turbidity maxima; numerical simulation;

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1 Introduction

Hydrodynamic and sediment transport processes in estuaries are very complex due to

the presence of irregular coastlines, islands, shoals, channels, and anthropogenic

structures, mixing fresh and saline water, river runoff, tides, winds, waves, and

offshore currents. Understanding these coastal processes is of great importance for

nearshore structure design, environmental protection, and disaster prediction and

prevention.

The estuarine turbidity maximum (ETM) or turbidity maximum (TM), characterized

by higher elevated turbidity or suspended sediment concentrations (SSC) than that

observed further landward or seaward, which has been reported in many estuaries

throughout the world, such as the upper Chesapeake Bay [Schubel, 1968], the Tamar

Estuary [Uncles and Stephens, 1993], and the Hudson River Estuary [Traykovski et al.,

2004]. The mechanisms of particle trapping in the turbidity zone are complex, with

two of them proposed as fundamental. The first involves the residual currents

associated with gravitational circulation in partially mixed estuaries, with the high

suspended sediment concentration often reported to be located near the landward limit

of salt intrusion [Postma, 1967]. Suspended matter flowing seaward on the surface

settles in a near-bottom layer where it is carried landward by an upstream residual

flow. The suspended matter is trapped and then accumulated at the convergence of the

near-bottom flow due to the estuarine circulation [Dronkers, 1986]. The second

mechanism is related to tidal distortion (in particular asymmetry in current velocities)

induced by non-linear interactions, as the ETM varies through the tidal cycle due to

resuspension and deposition [Uncles et al., 1985]. A tidal wave travelling into shallow

water typically generates strong landward currents, which usually results in an

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upstream sediment flux towards the head of the estuary, up to a tide decay zone,

where river flows dominate in sediment transport [Allen et al., 1980]. The ETM is

then to be found somewhere landward of the point where the tide becomes notably

distorted [Dyer, 1986]. Another process for the ETM formation was identified by Jay

and Musiak [1994]: internal tidal asymmetry or tidal-mixing asymmetry; however,

this mechanism appears to be not necessary for the existence of a stable ETM, and

affects the ETM formation only quantitatively but not qualitatively [Burchard and

Baumert, 1998]. In estuaries, strain-induced periodic stratification [Simpson et al.,

1990] is a dominant mechanism creating tidal mixing asymmetry in the presence of a

longitudinal density gradient. Tidal currents stratify the water column through the

straining of the density field during ebb tides, but destratify it during flood tides,

which leads to a residual flow seaward near the surface and landward near the bottom.

As a consequence, an upstream net transport of suspended sediment can be generated

by this mechanism [Geyer, 1993]. Cheng et al. [2011] also found that in some regime

of the estuary, the asymmetric-tidal-mixing induced flow may even be greater than

that of density-driven flow under weak stratification and tends to be smaller under

strong stratification.

In addition, other tidal effects are also confirmed to favour sediment trapping, such as

topographical effects [e.g. Friedrichs et al., 1998; Geyer et al., 1998], lag effects

(scour lag and settling lag) [e.g. Postma, 1961; Bartholdy, 2000; Burchard et al.,

2008], and asymmetry in flocculation processes [e.g. Scully and Friedrichs, 2007;

Winterwerp, 2011].

Since Festa and Hansen [1978], who confirmed the first mechanism mentioned above

by means of a steady-state two-dimensional numerical model, modelling of ETMs

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generally enabled the location and magnitude to be correctly simulated. Thus, effects

of multiple physical mechanisms involved in the ETM formation can be further

investigated [e.g. Dyer and Evans, 1989; Lang et al., 1989; Jay and Musiak, 1994;

Burchard and Baumert, 1998; Geyer et al., 1998; Brenon and Hir, 1999; Burchard et

al., 2004; Warner et al., 2007; Park et al., 2008; Xu et al., 2010].

Considerable numerical modelling of the Yangtze River Estuary (YRE) has been

carried out in recent years, most of which were focused on the hydrodynamics, such

as salt water intrusion [e.g. Qiu et al., 2012; Xue et al., 2009], transport time [e.g.

Wang et al., 2010; Li et al., 2011], and storm surges [e.g. Hu et al., 2009]; little

involved suspended sediment transport processes. On the other hand, most previous

studies of the suspended sediment transport and the ETMs in the YRE have been

based on field work [e.g. Su and Wang, 1986; Shen et al., 1993; Shi et al., 1997; Li

and Zhang, 1998; Chen et al., 1999; Shi et al., 2006; Wu et al., 2006; Gao et al., 2008;

Liu et al., 2010; Liu et al., 2011; Wu et al., 2012; Jiang et al., 2013]. Shi [2010] used a

one-dimensional vertical model to study the fine suspended sediment distribution at

the South Channel-North Passage of the partially mixed YRE. Subsequently, a two-

dimensional numerical model was established to study the characteristics of tidal flow

and suspended sediment concentration in the same region [Shi et al., 2010]. However,

the depth-integrated momentum and convection-diffusion equations are unable to

fully account for the effect of the complex topographic variations and baroclinic

hydrodynamics in the YRE. Jiang et al. [2013] gave an analytical model to derive

residual flow components and their contributions to the along-channel net sediment

transport. However, the vertically uniform eddy viscosity coefficients used in their

model cannot represent the variation on the vertical structure of turbulent mixing, e.g.

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changes between a well-mixed estuary and a highly-stratified estuary from spring to

neap tide [Song et al., 2013].

The construction of the Deepwater Navigation Channel (DNC) project, which started

in 1998 and was completed in 2011 (Figure 1), has significantly changed the

morphodynamics and hydrodynamics of the North Passage. The project created a 92-

km-long channel with a water depth of 12.5 m below the mean lowest low water

(MLLW) along the North Passage and South Channel. In addition, two dikes of length

48.1 km to the south of the channel and 49.2 km to the north, and 19 groynes, 30 km

in total length, were constructed to increase current speed and decrease sediment

deposition in the North Passage [Liu et al., 2011]. The flow pattern along the main

channel of the North Passage changed from a rotational current into almost rectilinear

flow due to the construction of dikes and groynes, and geometrically-controlled

eddies were produced in the groyne areas. Jiang et al. [2013] found that the amplitude

of M2 tidal current considerably increased and the residual flow structure was

significantly altered since the engineering works. Model simulations also reveal

significant velocity increases due to the constraining effect of dikes in the down-

channel section but small changes in the up-channel section [Ge et al., 2011]. In

addition, the saltwater intrusion in the project area was intensified at the up-channel

section but reduced at the down-channel section [Zhu et al., 2006]. Furthermore, the

construction of two dikes has cut off the horizontal sediment transport between the

North Channel and South Passage; thus, the suspended sediment transport and

associated ETM formation in the North Passage has likely altered. It is important to

understand the physical mechanisms resulting in the sediment trapping in the DNC

and how these mechanisms are influenced by the anthropogenic changes to the system.

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In Part I of this study [Song et al., 2013], we found spring-neap and flood-ebb tidal

variations in suspended sediment in the DNC, and proposed that the highly turbid

water intruding into the DNC on flood tides is related to the ETM movement. To

support our hypothesis, a numerical model is needed to interpret the hydrodynamics

and sediment transport dynamics of this study region as our observations are based

only on measurements in a single location in the middle of the DNC. Therefore, in

Part II of this paper, we have developed a three-dimensional wave-current-sediment

coupled coastal ocean model to study suspended sediment transport in the DNC,

North Passage of the YRE, in the dry season 2009, when the dikes and groynes were

completed, and the DNC was already dredged to 10.5 m below the MLLW. The main

aim of the present paper is to find out the possible reasons that may have caused the

siltation problem in the DNC. Additionally the following science questions will be

addressed: (a) physical mechanisms resulting in the ETM formation in the DNC; (b)

influences on suspended sediment transport by the anthropogenic changes; (c)

interaction between turbidity-driven and salinity-driven flows; (d) effects of external

forcings i.e. river discharges, waves, and winds on the sediment transport and

sediment trapping in the DNC. This paper is arranged as follows. The configuration

and development of the numerical model are described in Section 2, and followed by

model results and a discussion in Section 3. Finally, conclusions of this study are

presented in Section 4.

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2 Model descriptions

2.1 Hydrodynamic model

The model used here is the three-dimensional Princeton Ocean Model (POM); it

solves the primitive equations for momentum, temperature, and salinity on a

horizontal Arakawa C-grid and a vertical σ-coordinate system [Blumberg and Mellor,

1987; Mellor, 2004]. The level 2.5 turbulence closure scheme described by Mellor

and Yamada [1974, 1982] and Mellor [2001] is used to compute the vertical mixing

processes. The Smagorinsky diffusion scheme is used to calculated horizontal

diffusivity, assuming that the horizontal diffusivity of momentum, temperature, and

salinity are equal. The full set of model equations is described in Mellor [2004]. In the

latest version (POM08), the wetting and drying (WAD) scheme is incorporated into

the hydrodynamic model [Oey, 2005 and 2006].

Considering the price of computation time and data storage, the model area is given

from 121.0°E to 123.0°E in longitude and 30.6°N to 31.9°N in latitude, with variable

resolution from about 400 m × 400 m in the DNC region to about 2000 m × 2000 m

near the open boundaries (Figure 1). Consecutive grids roughly along the two dikes

are masked in the model and a no-slip condition is applied. In the DNC, it allocates

about 15 grid-cells in the cross-channel direction, which is sufficient to distinguish the

groynes and shoal areas in this area. In addition, the field measurements in the dry

season (March 2008) by Wu et al. [2012], illustrate a 20-km-long salt-front in the

DNC with salinity ranging from 6 to 20 psu, and also a 20-km-wide ETM with the

highest SSC of 2.5 kg·m-3 in the centre, which indicates that the longitudinal model-

resolution is also sufficient to represent the salinity-gradient and turbidity-gradient in

the DNC. In the vertical dimension, 16 sigma layers are used with five
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logarithmically-spaced layers near the bottom and another five near the surface to

obtain finer resolution in these layers. Tidal forcing with eight primary tidal

constituents (M2, S2, N2, K2, K1, O1, P1, and Q1) and two shallow water tides (M4 and

MS4) are used at the open boundaries, in which the nodal modulation corrections and

the astronomical argument for tidal constituents are included. The Yangtze River

runoff is included as an inflow boundary condition by using the daily-measured river

discharge during the simulation period at the Datong hydrologic station, about 600 km

upstream from the YRE. Monthly averaged salinity for the open boundaries is taken

from the re-analysed ARIVO (Analysis, Reconstruction, Indices of the Variability of

the Ocean) gridded fields produced at Laboratoire de Physique des Oceans (available

at http://wwz.ifremer.fr/lpo/SO-Argo/Products/Global-Ocean-T-S/Monthly-fields-

2004-2010). This ARGO dataset is monitored on a monthly basis, and merged with

other available measurements to produce gridded fields. Salinity at the upstream

boundary is given 1 psu. Constant temperature (10 ºC) is used as the initial condition

and the open/upstream boundary condition. The heat fluxes are assumed to vanish at

the sea surface, and the heat and salt is adiabatic at the bottom. In this study, to limit

the nonphysical mixing of the sharp horizontal salinity gradient, the horizontal

diffusivity for salinity is set to be zero.

2.2 Sediment transport model

If we assume that the horizontal velocity of the sediment is the same as that of the

water and that the vertical velocity of the sediment only differs from the water

velocity by the settling velocity, the three-dimensional sediment transport equation in

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the water column, based on the conservation equation for temperature or salinity in a

sigma coordinate system [Wang, 2002], can be written as:

      K h C 
 CD    CuD    CvD   C  w  ws    , (1)
t x y    D  

where t is the time; C is the SSC; D = H + η is the water depth with H the bottom

topography and η the surface elevation; u, v are the eastward velocity and northward

velocities, respectively; w is the vertical velocity component normal to the σ surface;

ws is the particle settling velocity; and Kh is the vertical diffusivity. According to

Wang and Pinardi [2002], ws is not affected by the transformation of coordinates

from a Cartesian coordinate system to the σ coordinate system. For the sediment

advection terms in equation (1), a first-order iterative upstream scheme was used,

which reduces implicit diffusion with an anti-diffusive velocity [Smolarkiewicz, 1984].

To couple the sediment transport model with the hydrodynamic model, a WAD

scheme for sediment transport is also necessary. In this study, assuming that the

sediment deposited on tidal flats dewaters rapidly, no SSC value is given for dry cells,

where the erosion and deposition processes also cease. The effect of SSC on the

equation of state is introduced by using a bulk-density relation [Adams and Weatherly,

1981]:

 w 
   w  1  C , (2)
 s 

where ρw is the seawater density, and ρs is the sediment bulk density.

In highly turbid systems, suppression of turbulence due to turbidity-induced

stratification leads to rapid accumulation of sediment in fluid mud layers [Allen et al.,

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1980] and enhancement of sediment trapping at ETM regions [Geyer, 1993]. Based

on numerical simulations, Wang et al. [2005] also showed that the sediment-induced

stratification in the bottom boundary layer (BBL) reduces the vertical eddy viscosity

and bottom shear stress in comparison with the model prediction in a neutrally

stratified BBL. In response to these apparent reductions, the simulated tidal current

shear in the water column is increased in their idealized estuary and on the western tip

of southwest Korea [Byun and Wang, 2005]. Nevertheless, the phenomenon of drag

reduction adjacent to the bed has been observed in sediment-laden flows [e.g. King

and Wolanski, 1996; Dyer et al., 2004]. Wang [2002] introduced a flux Richardson

number into the bottom friction coefficient Cd, which allows for the effect of

sediment-induced BBL stratification in the model:

2
  
Cd    , (3)
 1  AR f  ln  zb z0b  

where κ is the von Kármán constant, zb is the near-bottom layer thickness, z0b is the

bottom roughness, A = 5.5 is an empirical constant, and Rf is the flux Richardson

number, an index of the vertical density stratification in the Mellor-Yamada Level 2

approximation.

No sediment flux is allowed at the water surface, so that

K h C
 Cws  0 as   0 . (4)
D 

Sediment flux at the bottom is the difference between the deposition and erosion rates,

giving

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K h C
 Cws  Eb as   1 , (5)
D 

where Eb is the net sediment flux at the bottom due to erosion and deposition. The

algorithms for Eb are given by Ariathurai and Krone [1976]:

  b 
 E0   1 if  b   ce erosion
   ce 
Eb   , (6)
  b 
Cb ws 1    if  b   cd deposition
  cd 

where E0 is the empirical erosion coefficient, Cb is the SSC near the BBL, τb is the

bottom shear stress, τce and τcd is the critical shear-stress for erosion and deposition,

respectively; note that ws is negative as positive z is upwards. According to Ariathurai

and Krone [1976], the critical shear-stress for deposition may be the same or less than

for erosion.

The critical shear-stress for erosion, deposition, and the empirical erosion rate

coefficient are the parameters difficult to be determined in estuaries since they may

have a wide range of values within any one region. It depends on consolidation of the

bed, which is influenced by interactions with physical, biological, and chemical

factors, together with sediment composition [Houwing and Rijn, 1998]. Given the

complexity of the sediment erosion and deposition processes and the lack of field

measurements in the study area, constant value for τce, τcd, and E0 was chosen through

evaluation of model skill score (see below in Section 3.1). Together with settling

velocity, combination of these parameters summarized in Table 1 gives the highest

skill score for SSC simulation, where values were tested for τce and τcd ranging from

0.01 to 1.0 kg·m-1s-2, and for E0 ranging from 1.0×10-6 to 2.0×10-4 kg·m-2s-1.

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In POM, the calculation of the three-dimensional (internal) variables is separated into

a vertical-diffusion time step and an advection-plus-horizontal-diffusion time step

[Mellor, 2004]. The former is implicit, and solved by subroutine PROFT, whereas the

latter is explicit and solved by subroutine ADVT. In contrast to Wang [2002], in this

study the term associated with ws is solved in the subroutine for vertical diffusion

rather than in the advection subroutine, which gives a more accurate description of the

bottom and surface boundary condition. In addition, as ws is a function of SSC in this

study (discussed below in Section 2.4), it should be placed in the same elevation as

SSC at each vertical layer in POM, which is different from w, necessitating

interpolation (see Appendix A for details).

2.3 Wave model

The Simulating WAves Nearshore (SWAN) model [Booij et al., 1999] driven by sea

surface wind (6-hourly, and a 0.5º × 0.5º grid) obtained from QSCAT/NCEP Blended

Ocean Winds from Colorado Research Associates (version 5.0, which is available at

http://rda.ucar.edu/datasets/ds744.4/) is used to supply wave parameters for the

hydrodynamic model. The SWAN model, driven by satellite-measured sea surface

wind, was run first for the entire East China Seas (ECS) region, from 115.5ºE to

132.5ºE in longitude and 22.5ºN to 43.5ºN in latitude, with 5' × 5' spatial-resolution

(Figure 1). Then, wave parameters were calculated by SWAN on the YRE

hydrodynamic-model mesh-grid, with wave boundary conditions supplied by the ECS

SWAN model. Finally, the results were coupled one-way to the hydrodynamic model.

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The surface boundary condition for wind stress is modified through Xie et al. [2001];

while those for turbulent kinetic energy (TKE) and the mixing length as a result of

wave-breaking are given according to Mellor and Blumberg [2004] (see Appendix B

for details). In the shallow YRE, the combined effect of waves and currents on the

bottom stress, which determines the resuspension rate for suspended sediment, may

be significant. Here the wave-current BBL model of Madsen [1994] is implemented

to present the shear stress enhanced by the nonlinear interaction of waves and currents

in the BBL (see Appendix C for details).

2.4 Flocculation processes

Flocculation and deflocculation has an important impact on the transport of fine

grained cohesive sediments in ETM through associated increases in the settling

velocity of the sediment. Decades of efforts have been made to parameterize the

flocculation and floc breakup processes [e.g. Hawley, 1982; Gibbs, 1985; Dyer, 1989;

Kranenburg, 1994; Winterwerp, 1998 and 2002; Winterwerp et al., 2006; van Leussen,

2011]; however, due to the uncertainties in the formulations, some poorly known

empirical parameters are usually involved. In those formulae, the SSC and turbulent

shear stress (or TKE to be more accurate [Winterwerp et al., 2006]) are the dominant

physical parameters and control the flocculation and hence the settling properties of

mud flocs in suspension in the YRE [Shi, 2010]. The latest survey showed that the

median dispersed-grain sizes are 7-11 μm in the YRE, whereas in situ floc mean-

diameters range from 50-120 μm [Guo and He, 2011]. They also found that the flocs

formed in freshwater environments are not necessarily smaller than those formed in

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saline water, and can be larger. Therefore, the salt flocculation may play a minor role

in the YRE, if any.

From Mehta and McAnally [2008], the following expression is used for settling

velocity:

 ws 0 C  C0

ws   m1C n1 , (7)
 (C 2  m 2 ) n2 C  C0
 2

where ws0 is the free settling velocity; C0 is the critical concentration for flocculation,

and m1, m2, n1, and n2 are empirical settling coefficients. It includes several essential

physical processes, i.e. free settling, flocculated settling, and hindered settling. The

suspended particles begin to flocculate when SSC exceeds C0. Once it increases and

the flocculation processes are inhabited, hindered settling occurs. This is due to the

low permeability coupled with increased buoyancy and viscosity of the sediment-

water mixture. Hence it reduces the ability of the interstitial water to escape upwards

easily. TKE is not involved in this flocculation model, as no empirical coefficients for

this parameter have been obtained and validated from measurements in the YRE at

current stage. Field measurements show that the sand/silt/clay proportions and the

mean-diameters of sediment has a spatial variability in the YRE [Liu et al., 2010],

which cannot be well represented in this numerical model; thus a single set of

parameters is used to describe the sediment properties in order to keep the model

manageable. The coefficients in equation (7) used for the YRE model (some

evaluated using model skill score) are also summarized in Table 1.

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3 Model results and discussion

3.1 Model validation

To obtain the initial value of salinity in the model region, it was first spun up for one

year with climatologically monthly-averaged river discharge and salinity at the open

boundaries. It was verified that this spin-up time is sufficient for salinity in the YRE

to reach a near-equilibrium state, which is independent of the initial salinity

distribution. Then the model was run for another 40 days. This is marked as Case 0

for the standard run.

First we compare the simulated primary tidal harmonic constants with observed at

eight tide stations in the modal region (Figure 1). The root-mean-square (RMS) errors

of the four main constituents indicate that the simulated tides are acceptable. The

errors in amplitude are all under 10%, and in phase less than 10° (See Table 2 for

details). Then the model skill score (SS) is adopted to quantify the model errors with

the field measurements introduced in Part I of this study [Song et al., 2013]. The SS is

defined as the ratio of the RMS error normalized by the standard deviation of the

observation [Murphy 1988],

 X  X obs 
2

SS  1  mod
, (8)
 X 
2
obs  X obs

where X is the variable being evaluated and X is the temporal average. For reference,

an evaluation of a hydrodynamic and ecosystem model in the southern North Sea

categorized an SS > 0.65 as an excellent simulation, 0.5 to 0.65 as very good, 0.2 to

0.5 as good, and <0.2 as poor [Allen et al., 2007].

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In addition to the SS, the correlation coefficient (CC) between model and in-situ

observations (see Part I of this study [Song et al., 2013]) is also used to quantify the

model results:

CC 
 X mod  X
 X mod obs  X obs  . (9)
   X  
2 12

 X mod  X mod
2
 X obs
 obs

The SS and CC for the tidal elevation is 0.951 and 0.983, respectively (comparison

results are summarized in Table 3), although the simulated tidal range is a little larger

than observation (Figure 2a). To the simulated current velocity at 0.62 meters above

bed (mab), the SS for the eastward and northward velocity component is 0.872 and

0.752, respectively (Figures 2b and 2c); and the CC is 0.949 and 0.893, respectively.

In addition to the bottom velocities, we compare the model results with the velocity

structure recorded by the ADCPs (see Part I of this study [Song et al., 2013]) by

summing the velocity data over time and depth. SSs and CCs for current velocity

profiles are higher than for the bottom velocities: SS = 0.942 and CC = 0.974 for

eastward component; SS = 0.907 and CC = 0.958 for northward component. It

indicates the model well reproduces the vertical structures of the tidal current.

Model results of bottom salinity at 1.72 mab and SSC at 0.62 mab are also compared

with the measurements and shown in Figures 2d and 2e. The SS is 0.885 for bottom

salinity with CC = 0.944, and is 0.352 for bottom SSC with CC = 0.642. The

relatively lower SS and CC for SSC are mainly caused by the overestimation of

deposition during low slack water, and the absence of high-frequency oscillation as

observed. The failure to simulate the SSC fast-falling events during neap low slack

waters may be due to the possible underestimation of stratification within the BBL at

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those times and hence slight overestimation of the lutocline height. In addition, we

compare the model results with the vertical structures of salinity and SSC recorded by

the CTDs for a spring-tidal day (Julian day 88.25-89.25) and a neap-tidal day (Julian

day 92.92-93.92), respectively, through summing the data over time and depth. To the

spring tides, we obtain SS = 0.836 and CC = 0.942 for salinity, and SS = 0.342 and

CC = 0.851 for SSC; while to the neap tides, SS = 0.848 and CC = 0.938 for salinity,

and SS = 0.301 and CC = 0.811 for SSC. Noted that the SSC was equidistantly

measured in the vertical and most measurements are over the lutocline, therefore the

SS for SSC is mainly determined by the upper water column, which actually cannot

represent the situation in the bottom layers. Here, the vertical profiles of salinity and

SSC are plotted between observation and simulation at site A0 as a supplement (see

Figure 3; note that the tripod measurements near the bottom are also included in these

profiles), which indicates good agreement between the model results and observations.

Overall, the validation indicates an excellent tidal simulation and salinity simulation;

however, the simulations of SSC are good in their tidal variations (higher in CCs) but

not as accurate as the simulated tides and salinity in quantity. In general, the model is

able to reproduce the vertical structure of salinity and SSC, i.e. the landward

movement of the bottom salt and the lutocline on neap tides, and the spring-neap

variations between a well-mixed estuary and a highly-stratified estuary (Figures 4a

and 4b). In addition, the monthly-averaged erosion/deposition rate based on equation

(6) indicates siltation occurring in the middle-channel section (Figure 4g), which is

consistent with the filed measurement in Liu et al. [2011]. The main aims of this study

are to explain the physical mechanisms on sediment transport in a qualitative manner,

-18-
rather than a quantitative prediction; thus we believe the model is still applicable and

valuable to study the suspended sediment transport in the DNC.

3.2 Suspended sediment transport and turbidity maxima formation

The sediment transport and distribution shows strong variation between spring and

neap tides in the vertical (Figures 4a and 4b) and also in the horizontal (Figures 5a

and 5b). TMs are generated near the sand bar areas (Hengsha Shoalwater and

Jiuduansha Shoalwater), where the SSC is much higher than that in the DNC due to

the separation of the two dikes. The bottom SSC along the DNC is plotted in Figure

6a covering spring tides to neap tides. On spring ebb tides, high-turbidity water in

Hengsha Shoalwater, moving southeastward along the north dike by the residual

current, can spill over its east head, and form a relatively high SSC region at the DNC

outlet. This is one of the important sources for ETM formation and maintenance in the

DNC. On the following flood tides, tidal currents move this highly-turbid water

upstream, but the connection between this water and the TM at Hengsha Shoalwater

has been cut off by the north dike. Hence in the DNC an independent water mass with

high SSC (i.e. an ETM) is formed (Figure 4a). At high slack water, the settling of

suspended matter slightly increases the bottom SSC; the core reaches as far as

Channel Cell O (Figure 6a, channel cell labels can also be found in Figure 1). In the

ebbing tidal phase, a stronger current flushes the sediment out of the DNC; the ETM

moves downstream and decreases in magnitude (Figure 6a). As the water level falls,

flow velocity is decreased in the segments sheltered by groynes, giving the suspended

sediment more chance to be deposited (Figure 5a). At the low slack water, the spill-

-19-
over-mechanism continues to reinforce the upstream sediment transport and hence to

maintain the ETM in the DNC.

During neap tides, due to the reduced tidal current strength and intensified

stratification, less sediment is suspended and mixed to the upper layer than during

spring tides (Figure 4b), which generates much more turbid waters near bed (or fluid

muds). The net sediment flux (Figure 5b) indicates both the turbid waters from

Hengsha Shoalwater and Jiuduansha Shoalwater can flow into the DNC, forming a

highly-stratified sediment-tongue rather than an ETM. The stratified BBL reduces the

mixing, thus encouraging flocculation of sediment particles in the hyperpycnal flow

[Wang and Wang, 2010]. The bottom water in the turbidity zone is hence further

stratified by the SSC and a lutocline develops (Figure 4b). Due to the weak tidal

excursion, the sediment-tongue resides in the down-channel section during the entire

tidal cycle (Figure 6a).

The tidally-averaged suspended sediment flux demonstrates that the residual flow

traps suspended matters (Figures 5a and 5b). Following Cheng et al. [2011], we

decompose the along-channel Eulerian residual current into estuarine gravitational

circulation (summation of river-induced flow and density-driven flow, see Figures 7a

and 7b) and asymmetric-tidal-mixing-induced flow (Figures 7c and 7d). Both

components can generate a downstream flow on the surface but an upstream flow near

bottom. On spring tides, the estuarine gravitational circulation has a smaller

magnitude in upstream currents than the asymmetric-tidal-mixing-induced flow;

however, on neap tides, the former outweighs the latter. Thus, both the estuarine

gravitational circulation and the internal tidal asymmetry play roles in the sediment

trapping on spring tides, but the latter is a little more important in the net upstream

-20-
sediment transport; on neap tides, the gravitational-circulation is dominant in

producing the high SSC tongue.

Besides abovementioned two mechanisms, the role of tidal velocity asymmetry in the

turbidity maxima formation also needs to be investigated. To quantify its relevance to

sediment transport, Nidzieko and Ralston [2012] used sampling skewness of tidal-

current velocity (the third moment about zero, normalized by the second moment

about zero to the 3/2 power), as sediment transport is roughly proportional to velocity

cubed. Here we extend this method by means of harmonic amplitude and phase (see

Appendix D for details), in order to examine the origins of tidal velocity asymmetry

(i.e. the contribution of different tidal-constituent-combination [Song et al., 2011]).

Recall that the calculation gives a flood-dominant velocity skew when γ2(u) > 0 or

γ3(u) > 0 (i.e. an upstream net sediment transport), but an ebb-dominant velocity skew

when γ2(u) < 0 or γ3(u) < 0 (i.e. an downstream net sediment transport). In Part I of

this study [Song et al., 2013], M4 and MS4 have been found as the first two largest

contributors of tidal asymmetry. Here through the combination of different tidal

current constituents, it shows that both the pair of M2 and M4 (Figure 4d) and the

triplet of M2, S2, and MS4 (Figure 4e) can generate opposite asymmetric patterns

between up-channel and down-channel sections, which cause suspended sediment to

converge at around points J - N. Furthermore, as both γ2 and γ3 have maximum values

of 0.82 [Song et al., 2011], the moderate magnitudes (about 0.3) of γ2(u) and γ3(u) in

the DNC with a semi-diurnal regime, indicates that the tidal velocity asymmetry also

contributes a lot to the formation of the ETM in the DNC. If we include the residual

current in the tidal current skewness via equation (D3) in the Appendix D, we find

-21-
larger opposite velocity skews, as shown in Figure 4f. It indicates the residual flow

significantly enhances the velocity skews as well as the sediment trapping in the DNC.

Other mechanisms related to the suspended sediment transport can also be confirmed

by the model results. The amount of resuspension depends on the magnitude of the

near-bottom velocity, which tends to be higher during ebbing tides owing to the

offshore fluvial flow. Meanwhile, due to much longer period of low current velocities

around high tide (a smaller rate of velocity increase, as shown Figure 2b in Part I

[Song et al., 2013]) than around low tide, this slack-water asymmetry is responsible

for greater deposition of sediment due to sediment deposition during high slack water

than during low slack water (Figure 6a). During spring tidal cycles, despite the fact

that both estuarine gravitational circulation and asymmetric-tidal-mixing-induced

flow may produce the SSC tongue, a larger tidal excursion generates a stronger tidal

pumping effect, which dominates the landward suspended sediment transport in such

a partial-mixing estuary. This has already been shown with the observation in Part I of

this study [Song et al., 2013]. However, during neap tides, the strong stratification

generates onshore baroclinic flow, and its strong shear effect plays a more significant

role in the landward suspended sediment transport than the weak tidal-current

excursion.

3.3 Turbidity-driven flow

In the ETM region, the large SSCs significantly affect the vertical density structure,

leading to stratification and a reduction of mixing [Winterwerp, 2001], thereby

affecting, for example, the tidal wave propagation [Gabioux et al., 2005]. Talke et al.

-22-
[2009] developed a simple analytical model including salinity- and turbidity-induced

circulation from density gradients. They found that the turbidity-driven currents and

salinity-driven currents act together to enhance tidally averaged circulation upstream

of the ETM, but significantly reduce residual circulation downstream, where salinity

and turbidity gradients oppose each other. In Case 1, we take SSC out of the equation

of state for seawater density (i.e. remove equation (2) from the model computation) in

order to compare with the control run (Case 0), which considered the effects of

suspended sediment on the density field. Cases discussed here and below are

summarized in Table 4.

In Case 0 we consider the SSC contribution to seawater density and thus generated

turbidity effects. The direct turbidity effect is to establish a flow caused by a turbidity-

induced density-gradient. During spring tides, the turbidity-driven flow enhances the

vertical skew of the density-driven flow between surface and bottom (Figure 7e). In

addition, the turbidity-driven flow can also intensify the sediment trapping induced by

the internal tidal asymmetry (Figure 7g). Thus, an ETM with a greater magnitude in

Case 0 than Case 1 is expected (compare Figure 4a with Figure 8a). During neap tides,

the turbidity-driven flow enhances the salt intrusion (compare Figure 4b with Figure

8b) and largely increases the density-driven flow at the salt wedge (Figure 7f). The

bottom salt-shift intensifies the stability of stratification and reduces the intertidal

asymmetry of turbulent mixing (Figure 7h), which accelerates the suspended sediment

settling and generates strong vertical-turbidity-gradients within the BBL (compare

Figure 4b with Figure 8b). Note that the turbidity effect increases the vertical salinity-

gradients but not the horizontal salinity-gradients, which is actually reduced due to the

extension of the bottom salt-tongue. In addition, the magnitudes of TMs in shoal

-23-
waters are also much increased in Case 0, which enlarges the sediment transport into

the DNC (compare Figure 9a with Figure 9b), even though the TMs are closer to the

DNC outlet in Case 1.

Therefore, coupling SSC into density equation of state, the intensified onshore current

near the bottom pushes the salt front further landward, which increases the salinity-

induced stratification in the DNC. It in turn changes the suspended sediment transport

and enhances the sediment-induced stratification in the turbidity zone.

3.4 Influences of DNC project on suspended sediment transport

To study the impact of the DNC on suspended sediment transport in the North

Passage, another model (Case 2) is conducted with the same configuration as Case 0

but without the deepwater channel, dikes, and groynes. During spring tides, sediment

residual flux (Figure 5c) shows that an ETM in the North Passage is formed by the

convergence of the sediment transport between Jiuduansha Shoalwater and Hengsha

Shoalwater. Fine sediment is eroded and resuspended by strong tidal currents or wind

waves in those shallow waters, then brought into the North Passage, where most of it

is trapped in the deep middle-passage section (Figure 8d). Comparing the situations

before and after the DNC construction, the position of the ETM does not change too

much; the former has a greater magnitude but less diffuse turbidity-gradients than the

latter. During neap tides, the entire North Passage is occupied by highly-turbid waters

(Figure 5d). Fluid mud may also be generated, but the stratification is not as strong as

the situation after the DNC construction (Figure 8e).

-24-
The construction of dikes and groynes, and dredging of the deepwater channel

accelerated the fluvial flow on the surface, which dramatically reduced the maximum

flooding-current velocity and enhanced the ebb-dominance in the current (Figure not

shown). This constraining effect reduces the salt intrusion, which induces a less turbid

upper-channel section; however, the intensified stratification weakens the turbulent

mixing in the DNC. The DNC project indeed relieved the turbidity in the North

Passage, but it is not able to solve the silting problem completely (compare Figure 4c

with Figure 8f). The spill-over-mechanism replaces the cross-channel sediment

transport after the DNC project completion. The ETM still occurs at almost the same

position during the spring tides; while fluid mud still forms during the neap tides.

3.5 River discharge

The Yangtze River discharge has a strong seasonal variation, and even varies

significantly in the dry season, from about 10,000 m3s-1 in January to about 30,000

m3s-1 in March 2009. We do not have field measurements to validate our model in

flood seasons. Therefore, we only compare the situations with different river

discharges in the dry season. Two cases with constant river-discharge of 40,000 m3s-1

in Case 3 and 10,000 m3s-1 in Case 4, were run to show the influence of the river

runoff on suspended sediment transport in the DNC. The model configuration is the

same as Case 0, except for the river boundary conditions. In Case 0, we use the daily

measured river discharge at the Datong hydrologic station, which increased from

16,819 m3s-1 on March 1 to 28,277 m3s-1 on March 13 and then fell to 19,169 m3s-1 on

April 7, 2009, with an averaged-discharge of approximately 23,043 m3s-1.

-25-
In Case 3, the increased river discharge pushes the residual-flow convergence seaward;

the range of the salt-frontal zone is compacted as well as that of the ETM in the DNC

(compare Figure 10a with Figure 4c). The increased river discharge reduces the

magnitude of the ETM on spring tides and the sediment-tongue on neap tides;

however, the downstream flow can still not completely push the ETM out of the DNC.

This is because the increased fresh water also moves the TM in the Hengsha

Shoalwater further seaward in Case 3, in which it generates an even higher turbidity at

the DNC outlet through the spill-over-mechanism (compare Figure 9c with Figure 9a)

and thus may hinder the seaward movement of the ETM.

In Case 4, the tides are dominant in the entire DNC, when river runoff is low. None of

asymmetric-tidal-mixing-induced flow or the tidal velocity asymmetry could produce

effective sediment traps (i.e. convergent residual flows) in this channel (Figure 10b).

The TMs in Hengsha Shoalwater and Jiuduansha Shoalwater are not able to approach

the DNC outlet (Figure 9d), leaving a clean down-channel section in this case. The

turbid water in the up-channel section originates from the North Channel via the

channel between Changxing Island and Hengsha Island (Figure 1) or from the South

Channel via the DNC up-head.

Comparing these cases, we find that the ETM in the DNC can move over a channel-

scale range in different river-discharge conditions. The tide itself is insufficient to

generate strong convergent sediment flux in the DNC, which confirms the key role

played by the estuarine gravitational circulation in the ETM formation. On the other

hand, a larger river-discharge can move the ETM seaward, but cannot remove it from

the DNC as the non-local turbid water landward intrusion is also enhanced by the

larger river-discharge. This is consistent with the observations in 2008 [Wu et al.,

-26-
2012], in which a compact ETM occurred in the down-channel section during the

flood season.

3.6 Wave effects

The SWAN result shows a large bottom wave orbital velocity in the Hengsha

Shoalwater, where sediment can be suspended by waves and then transported by tidal

currents to the DNC outlet. To check the wave effects on the suspended sediment

transport in the North Passage region, we set up the following two cases. Different

from Case 0, in Case 5, the wave-breaking effects (see Appendix B for details), which

can enhance TKE dissipation on surface boundary layer [Stacey, 1999] and deepen

the surface boundary layer [Mellor and Blumberg, 2004], are taken out of the model.

In Case 6, the shear stress generated by current only (no waves) is considered. Grant

and Madsen [1979] has shown that the shear stress is altered because the turbulence

generated by the wave-current interaction near the bed is different from the stress

expected in the case of pure waves or pure currents. Therefore, the effects of wave-

current interaction in the BBL (see Appendix C for details) on the suspended

sediment transport can be investigated through the comparison between Case 6 and

Case 0.

In Case 5, the wave-breaking-induced mixing on the surface vanishes as shown in

Figure 11. It shows weak vertical diffusivity near the surface layer. In contrast, Case 0

shows great vertical diffusivity on the surface, and the layer depth gradually decreases

as the significant wave height reduces from the open sea to the DNC. The erodible

particles are less readily mixed to the surface layer in Case 5 but accumulate near the

-27-
bottom, which generates an ETM with relatively larger turbidity (compare Figure 10c

with Figure 10a). The increased stratification tilts the isohalines in the DNC and

enhances the bottom salt intrusion (Figure 10c).

In Case 6, without the bottom wave-current interaction, the SSC in the turbidity zone

is dramatically reduced (compare Figure 10d with Figure 10a) as well as the turbidity-

induced stratification especially in the BBL (Figure 10d), which reduces the bottom

salt intrusion. In this case, the ETM is located in the up-channel section, perfectly at

the salt wedge. It indicates that in this case the ETM is formed without the

interference of non-local turbid waters. As above mentioned, the wave-generated

bottom orbital velocity is rather small in the DNC, but significant in the Hengsha

Shoalwater and Jiuduansha Shoalwater, where are important origins of the trapped

suspended sediment in the ETM. The SSC in those shoalwaters is largely reduced

when the bottom wave-current interaction is neglected; so the turbid water intrusion is

also largely decreased or even disappears, and is hence unable to influence the ETM

formation in the DNC (Figure 6b).

These numerical experiments illustrate that the wave itself has little effect on salt

transport; however, the wave-suspended sediment could drive circulation, which

affects the salinity distribution and hence the salinity-induced flow, as we discussed in

3.3. In addition, the case comparison confirms that the turbid water intrusion play a

significant role in the ETM formation in the DNC. The surface wave-breaking-

induced mixing relieves the sediment trapping and siltation problem in the DNC.

-28-
3.7 Wind effects

The YRE has four southeastward outlets, which are favoured by southeasterly or

southerly winds to generate larger waves. To examine the wind effects on the

suspended sediment transport in the DNC, we established two cases with steady

northwesterly (Case 7) and southeasterly (Case 8) winds, respectively. For these two

cases, a constant wind speed of 10 ms-1 is assumed. To generate the corresponding

wave fields, we ran the ECS SWAN and YRE SWAN in sequence with the above

wind fields again. Then, the results were used in the hydrodynamic model. Figure 12

shows the horizontal distribution of the monthly-averaged significant wave height and

maximum bottom orbital velocity for Cases 0, 7, and 8. The significant wave height is

reduced with the decrease in water depth, but the maximum bottom orbital velocity is

increased. Southeasterly winds generate higher wave and larger bottom orbital

velocities than northwesterly winds. Correspondingly, the bottom SSC in Case 8 is

expected to be larger than that in Case 7 (Figures 13a and 13b).

In these two cases, the steady strong winds mixing the water column better than the

control run, especially in the surface layers (Figures 13a and 13b). The along-channel-

direction winds powerfully affect the residual flow (Figures 13c and 13d), which

changes the pattern of the ETM in the DNC. In Case 7, the northwesterly wind

enhances the downstream surface flow, which induces a stronger compensatory flow

near the bed than that in Case 0 (Figure 13c). In addition, the TMs outside the DNC

are moved offshore by the northwesterly wind, which increases the chance for turbid

water reaching the DNC outlet (compare Figure 9e with Figure 9a). Thus, the ETM

can be extended to the entire channel (Figure 13a). Conversely, the southeasterly wind

drives an upstream surface flow in Case 8, which reduces the downstream surface

-29-
currents and hence the upstream bottom compensatory-flow. Thus the convergent

estuarine gravitational circulation in the DNC is destroyed (Figure 13d). Although

more sediment is eroded for the bed by stronger waves, most of them cannot be

transported into the DNC, but deposit at the DNC outlet (Figure 9f).

These model runs illustrate that the wind-induced-wave affects the magnitude of

ETMs or TMs, and the wind-driven-circulation has a great influence on the ETM

location. It also confirms the importance of the estuarine gravitation circulation to the

ETM formation in the DNC.

4 Conclusions

To study suspended sediment transport in the Yangtze River Estuary, especially in the

Deepwater Navigation Channel, we establish a three-dimensional wave-current-

sediment coupled numerical model, which is validated with the in-situ data measured

in the DNC in late March and early April 2009 (details can be found in Part I of this

study [Song et al., 2013]). The model captures the major spring-neap asymmetric

patterns in salt transport and suspended sediment transport. The siltation in the DNC

is generated by the joint effect of the tidal-asymmetry-induced (tidal velocity

asymmetry and tidal mixing asymmetry) and the estuarine-gravitational-circulation-

induced convergence (Figures 4c and 4g). The residual flow decomposition indicates

that the estuarine gravitational circulation is dominant in the channel during neap tides;

however, the asymmetric-tidal-mixing-induced flow is comparable to or even greater

than the estuarine gravitational circulation during spring tides. Furthermore, a more

skewed tidal velocity asymmetry can be generated with the estuarine gravitational

-30-
circulation in the DNC. In addition, the low-river-discharge experiment (Case 4)

indicates that tide itself is insufficient to the ETM formation. Therefore, the estuarine

gravitational circulation plays the most important role in the ETM formation in the

DNC.

Different from most previous studies, non-local sediment also greatly contributes to

the mass of the observed deposits in the DNC through the spill-over-mechanism, in

addition to the redistribution of sediment due to local erosion and deposition and the

direct input of sediment from the river. Comparing these numerical experiments, we

find the turbidity zone is usually confined to the landward limit of the upstream flow

in all cases except case 6, in which the ETM locates further upstream than the

convergence point of residual current (Figure 10d) when the non-local sediment is

largely reduced (Figure 6b). However, in that case the ETM magnitude is largely

reduced. So the non-local sediment is the most important origins for sediment

trapping within the ETM, which also have significant influence on the ETM

magnitude and location.

The external forcings (i.e. river discharges, waves, and winds) give effects on both the

local environment and further afield. Due to the non-local sediment intrusion, ranking

the effects of different forcing mechanisms is rather complicated. The monthly- and

spatial-averaged bed erosion rate and SSC in the DNC at each case is given in Table 4;

the latter indicates the suspended sediment trapped in the DNC. As shown, surface-

wave-breaking relieves the sediment trapping in the DNC, but the bottom wave-

current-interaction aggravates the bed erosion and elevates the SSC in the ETM;

compared to other cases, the former and the latter has the least and largest influence

on the suspended sediment transport (Table 4). The wind effects have a greater impact

-31-
on the sediment trapping in the DNC than the river discharges, as the wind-driven-

circulation has an influence on the turbidity of upstream net flow, as well as on the

magnitude of upstream net flow. These two cooperate with each other, for instance,

the steady northwesterly wind moves the TMs downstream, increasing the turbidity of

intrusion water; meanwhile, it enhances the bottom compensatory flow in the DNC,

taking more sediment into the DNC. The river discharge transports suspended

sediment offshore both in the DNC and in the shoalwaters, but the latter could

generate stronger non-local sediment intrusion into the DNC, which moves against the

former. Thus, the river discharge generally has the relatively small impact on the

sediment trapping in the DNC. Based on the bed erosion rates (Table 4) we find the

steady-northwesterly-wind condition favours the siltation in the DNC most.

The construction of the DNC project obstructs massive sediments being directly taken

into the passage from its edges. In addition, the constraining effect of the dikes and

the deepened channel increases the downstream flow, which moves the ETM offshore.

However, this project failed to stop the non-local sediment intrusion since the

constraining effect also intensifies the upstream flow. Therefore, the DNC project

reduces the magnitude of the ETM in the North Passage (the averaged SSC is largely

reduced in Table 4), but is not able to solve the silting problem completely (the bed

erosion rate is changed little in Table 4).

The YRE provides a good example of a turbid estuary, with SSCs over 4 kg·m-3 near

bed and over 30 kg·m-3 in fluid mud. The horizontal SSC gradient is usually

significant between tidal flats and channels. Thus, turbidity-driven flow cannot be

ignored in this study case. The model results confirm a positive feedback between

turbidity-driven flow and salinity-driven flow. When saline-water intrusion is

-32-
enhanced, the turbidity in the DNC will rise correspondingly, and vice versa.

Furthermore, the turbidity-driven flow suppresses the turbulent mixing in the BBL

and hence upper water column (Figure 11b), which increases the sediment settling

and deposition (Table 4). The effect of turbidity-driven flow on suspended sediment

transport may exist in any numerical case of this study due to its interaction with

salinity-driven flow and turbidity-induced stratification. By removing the turbidity-

driven flow completely out of the computation (i.e. Case 2), we find it even has a

larger impact on the sediment trapping than the river-discharge cases (Table 4).

The suspended sediment transport in the Deepwater Navigation Channel has three

different asymmetric patterns: flood-ebb tidal cycles; spring-neap tidal cycles; and

flood-dry seasons (the first two are studied in Part I [Song et al., 2013] and Part II of

this study; the last was observed by Wu et al. [2012] and Jiang et al. [2013]), which

indicates the complication of this estuarine system. Furthermore, given the importance

of wind and wind waves, a seasonal variation on the suspended sediment transport is

also expected due to the change of wind direction and magnitude by monsoon. With

the numerical models, we can explore the mechanisms and forcings on the suspended

sediment transport in this coastal system; however, the fate of the sediment might be

determined by more complex competition between different mechanisms, some of

which might be still unknown to us or can not be parameterized in numerical models.

-33-
Appendix A: Subroutine for the vertical diffusion of suspended sediment

concentration

To better represent the surface [equation (3)] and bottom [equation (4)] boundary

condition of equation (1), the term associated with settling velocity ws in equation (1)

is solved in the subroutine for vertical diffusion rather than that for advection. The

subroutine for vertical diffusion is based on equation (25) in Mellor [2004]:

D n1T n1  DT 1   T n1  R

 n1  Kh  , (A1)
2ti D     

where σ is the vertical coordinate, ∆ti is the internal mode time interval, D is the

water depth, T can be any three-dimensional variable, n is the time step, Kh is the

vertical diffusivity coefficient, R is the source or sink term, and DT is the temporal

results obtained from the subroutine for advection.

The finite difference with respect to σ of equation (A1) can be written as:

2ti  khk kh  2ti

fk  fk    f k 1  f k  k 1  f k  f k 1    rk  rk 1  , (A2)
dh  dzk  dzzk 1
2
dzzk  dh  dzk

where fk, khk, and rk are the suspended sediment concentration (SSC), vertical

diffusivity coefficient, and the product of fk and wsk in the k-th vertical grid,

respectively, dh is the internal mode water depth, dzk = zk – zk+1, where zk is the σ

coordinate for the k-th vertical grid index, dzzk = zzk – zzk+1, where zzk is the σ

coordinate intermediate between zk and zk+1, f k is the temporal SSC obtained from the

subroutine for advection. Equation (A2) is the same as equation (33) in Mellor [2004].

-34-
Note that rk needs to be interpolated to zk from zzk, as ws is a function of SSC, and

placed at the same elevation of SSC in the vertical, i.e. zzk.

rk  f k  wsk 
 fk  wsk  fk 1  wsk 1    zzk  zk  . (A3)
dzzk 1

To apply the surface boundary condition (k=1), we specify zero sediment flux, thus,

 f1  ti  r2  dh  dz1 
f1  , (A4)
a1  1

where

2ti  khk 1
ak   . (A5)
dh 2  dzk  dzzk

Near the bottom (k = kb – 1, kb is the vertical grid index at the bottom), the bed

erosion and deposition rate (Eb) is prescribed, so we get

ckb1  gg kb2  f kb1  2ti   rkb1  Eb   dh  dzkb1 

f kb 1  , (A6)
ckb1 1  eekb2   1

where

2ti  khk
ck   , (A7)
dh  dzk  dzzk 1
2

ak
eek  , (A8)
ak  ck  1  eek 1   1

ck  gg k 1  d k
gg k  , (A9)
ak  ck  1  eek 1   1

-35-
 2ti
and d k   f k   rk  rk 1  . (A10)
dh  dzk

-36-
Appendix B: Surface boundary condition for wave model coupling

The surface boundary condition for wind stress is modified via the surface roughness

in the presence of surface waves:

 s  a u*s u*s , (B1)

where τs is the wind stress, ρa is the air density, and u*s is the friction velocity:

u*s   u10 / ln  z / z0 s  , (B2)

where u10 is the wind speed at 10m above the sea surface, and z0s is the surface

roughness length. To estimate the effect of surface waves on wind stress, the

empirical model in Donelan et al. [1993] is proposed to compute the surface

roughness length [Xie et al., 2001]:

0.9
3.7 105 u10 2  u10 
z0 s    , (B3)
g  c p 

where cp is the wave speed corresponding to the spectral peak frequency and u10/cp is

the wave age.

The surface boundary condition for turbulent kinetic energy (TKE) takes account of

an enhanced source of turbulence in the surface layer due to wave breaking [Mellor

and Blumberg, 2004]:

q2  15.8 
2/3
u*2s at z=0, (B4)

where q2/2 is the TKE and α is a wave age dependent coefficient, given by Terray et

al. [1996] as
-37-
  15  c p u*s  exp   0.04 c p u*s   .
4
(B5)
 

Following Mellor and Blumberg [2004], the surface boundary condition for the

mixing length l is given as:

l  max lz ,  zw0  , zw0  0.85H s at z=0 or (B6a, b)

l  lz   z w 0 , zw0  1.60 H s at z=0, (B7a, b)

where lz is the mixing length computed using the Mellor-Yamada model, zw0 is a

wave-induced mixing length, and Hs is the significant wave height. In addition, we

assume an exponentially decaying wave-induced mixing length to express its vertical

variation:

zw  zw0  exp min  0,  H s  zd  , (B8)

where zd is the distance below the sea surface and λ is an empirical coefficient

determining the depth of mixing due to wind waves. Based on bubble observations

[Thorpe, 1984, 1992], the depth scale of the wave-induced turbulence in wave

breaking conditions is of the order of 4.0Hs (i.e. λ = 4.0).

-38-
Appendix C: Bottom boundary condition for wave model coupling

The wave-current bottom boundary layer (BBL) model is implemented based on

Madsen [1994]. The concept of this model is that the nonlinear interaction of the

surface waves and currents enhances the shear stress in a much thinner wave

boundary layer (WBL) that exists inside of the mean current-BBL. The shear velocity,

u*wc, inside the WBL, z < δwc, reflects the combined wave-current flow; outside the

WBL, z > δwc, but inside the current-BBL, the shear velocity is a function of the

averaged (over several wave periods) current shear velocity, u*c. Thus, the eddy

viscosity profile can be written as:

 u z for z   wc
K m   *wc , (C1)
 u*c z for z   wc

and the bottom shear stress τb is parameterized as:

u
Km  b  . (C2)
z

Based on the model of Madsen [1994], the maximum instantaneous shear stress for

the combined flow is the vector sum of the time-averaged instantaneous shear stress

induced by currents, τc, and the maximum shear stress associated with waves, τwm:

 b   c   wm . (C3)

Equation (C3) can be rewritten in terms of the magnitude of shear velocities:

u*2wc  C u*2wm , (C4)

where

-39-
 1/2
  u*c 
2
 u*c  
4

C  1  2   cos wc     , (C5)

  u*wm   u*wm  

with φwc the angle between the current direction and the direction of wave propagation.

A wave-current friction factor fwc was introduced to relate the magnitude of the

maximum shear stress for the wave, u*wm, to the magnitude of the near-bottom orbital

velocity, ubr:

1
u*2wm  f wcubr2 , (C6)
2

where fwc can be approximated by the following explicit formulas [Madsen, 1994]:

   C ubr 
0.078
 C u
 C exp 7.02    8.82  for 0.2<  br  102

   k N r  
k N r
f wc  . (C7)
   C ubr 
0.109
 C u
C exp 5.61   7.30 for 102 <  br  104

   k N r   k N r

Here, kN is the equivalent Nikuradse roughness of the bottom and ωr is the wave

radian frequency. In the numerical model, the bed quadratic-drag law is usually

calculated using the current velocity at the vertical mid-elevation of the bottom

computational cell, which may vary throughout the domain. For such a current

velocity ucr at a given elevation zr above the bed, the magnitude of current shear

velocities is given as [Madsen, 1994]:

u*wc ln  zr  wc   ln  wc z0b  ucr 

u*c   -1+ 1  4  for zr   wc , and (C8)
2 ln  wc z0b   ln  zr  wc  u*wc 


-40-
  ucr u*wc
u*c  for zr   wc , (C9)
ln  zr z0b 

where z0b = kN /30 is the bottom roughness length, and the WBL thickness δwc is

defined as:

 C ubr
2 u*wc r for k   8

 wc 
N r
. (C10)
k C u
for  br  8


N
k N r

An iterative procedure described by Madsen [1994] is applied to solve the magnitude

of τb by first assuming Cμ = 1.0 to obtain an initial estimate of u*wm from equations

(C6) and (C7) and u*c from equations (C8) – (C10). With these values, the Cμ are

updated using equation (C5) and the procedure repeated until convergence of fwc is

obtained to two significant digits.

-41-
Appendix D: Metrics to quantify velocity skew by using harmonic constants

The method introduced by Song et al. [2011] can be applied to derive metrics to

quantify velocity skew. However, in contrast to tidal elevation, tidal current is a two-

dimensional physical quantity (i.e. having magnitude and direction), which gives an

ellipse rather than a fluctuation; it is difficult to estimate velocity skew in direction as

well as strength. However, in most cases we are only concerned with the peak

velocity skew, which affects bedload transport and finer suspended-load erosion

through different peak flood/ebb shear stresses. Note that the skewness of peak

velocity is not simply related to the skewness of its components (e.g. eastward

component and northward component), as it is nonlinear. Here, we simplify the

situation to a special case of predominantly rectilinear currents (e.g. along-channel

current in narrow, long estuaries or cross-shore current on tidal flats), of which the

minor axis is very small. Thus, the current velocity can be expressed as the

summation of N individual constituents along its major axis:

N
u (t )  u0   un cos nt  n  , (D1)
n 1

where u0 is the residual current velocity, un is the major-axis length, ωn = 2π/Tn is the

frequency, Tn is the period and ψn is the phase of constituent n.

Since the bedload sediment transport is roughly proportional to velocity cubed,

Nidzieko and Ralston [2012] suggested that the mean velocity in the skewness be

calculated using of the sample third moment about zero, rather than about the mean.

Thus, the skewness of the tidal current can be expressed in terms of expectation

values:

-42-
  N
 
3

E   u0   u n  
E u t 
 
3

  u   33      n 1  
, (D2)

 
3/2 3/2
E u  t  
2
  N
 
2
   E   u0   u n   
    
  n 1

Analogous to the work in Song et al. [2011], we expand equation (D2) and remove

those terms which are oscillatory about zero and have an expectation value of zero

over a long time.

The non-zero expectations are only be produced by the mean velocity and those

combinations of two or three constituents with a frequency relationship of 2ω1 = ω2 or

ω1 + ω2 = ω3. Then, the skewness of u can be written as:

ui u j uk cos  i   j  k    ui2u j cos  2 i  j 

3 N 3 3
u03  u0  ui  
2 i 1 i  j k 2 2i  j 4

 N u   i j k
3/2
.
 2 1 N 2
 u0  2  ui 
 i 1 

(D3)

The longer ebb duration is usually accompanied by stronger flood-current velocities

and a longer flood duration with stronger ebb current velocities, as expected from

mass conservation, provided u0 is small. There is no tidal frequency information

included in equation (D3), and the residual flow (e.g. fluvial discharge or coastal

circulation) contributes to the velocity skew through the net velocity term (the first

term in the numerator on the right-hand side of equation (D3)) and its interaction with

the tidal constituents (the second term in the numerator on the right-hand side of

equation (D3)). This might alter the total direction of velocity skew generated by pure

tides. Neglecting the residual flow, if currents and elevation are exactly in quadrature,
-43-
fast-rising tides require flood-dominant velocities to convey the tidal prism in a

shorter period and vice versa.

In the absence of residual current, the velocity skew created by the addition of two (N

= 2) or three (N = 3) frequency-related constituents is:

3 2
u1 u2 cos  2 1  2 
 2 u   4 3/2 , (D4)
1 2 
 2  u1  u2  
2

and

3
u1u2u3 cos  1   2  3 
 3 u   2 3/2 , (D5)
1 2 2 
 2  u1  u2  u3  
2

respectively, where 2ω1 = ω2 in equation (D4) and ω1 + ω2 = ω3 in equation (D5).

Equation (D4) can be used to quantify velocity skew caused by one constituent and its

first harmonic constituent, e.g. M2 and M4 in shallow water. The skew caused by

triple constituents (e.g. O1, K1, and M2) can be quantified by equation (D5). The

relative phase, 2ψ1 – ψ2 and ψ1 + ψ2 – ψ3, is the only phase information retained in

equation (D4) and equation (D5), respectively, and determines the direction of

velocity skew. A symmetric tide has a relative phase 2ψ1 – ψ2 of ±90º. If −90º < 2ψ1–

ψ2 < 90º, then γ2(u) > 0 and the distorted composite tide typically has more in the

quantity of ebb current samples (by definition positive values of u indicate an onshore

direction), which indicates a greater maximum flood-current velocity (i.e. flood

dominance) due to mass conservation. If 90º < 2ψ1 – ψ2 < 270º, the relationship is

reversed, typically resulting in an ebb-dominant tidal current [γ2(u) < 0]. Similarly,

-44-
−90 º < ψ1 + ψ2 – ψ3 < 90º indicates a flood-dominant current velocity [γ3(u) > 0], and

90º < ψ1 + ψ2 – ψ3 < 270º indicates a greater maximum ebb-current velocity [γ3(u) <

0]. In addition, the relative phase ψ1 + ψ2 – ψ3 = ±90º shows a symmetric tide current.

-45-
Acknowledgments

D. Song has been supported by the China Scholarship Council and the University of

New South Wales (UNSW) Top-up Scholarship for his PhD study in Australia. X. H.

Wang was supported by 2011 Australian Research Council/Linkage Projects

(LP110100652). This paper benefited from reviews by Dr. Andrew Kiss and Dr. Peter

McIntyre at UNSW Canberra, and two anonymous reviewers’ constructive comments

and thorough reviewing. Computational and storage resources used in this work were

provided by the National Computational Infrastructure National Facility in Canberra,

Australia, which is supported by the Australian Commonwealth Government. This is

a publication of the Sino-Australian Research Centre for Coastal Management, paper

number 16.

-46-
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Figure Captions:

Figure 1. Bathymetry map of the Yangtze River Estuary with detailed structure of the
Deepwater Navigation Channel project including channel cell names and groyne
numbers. In the middle figure, the red star gives the quadrapod position and the
numbered blue dots show the tide stations for model validation. The top figure shows
the intensified mesh grid around the region of the Deep Navigation Channel project.

Figure 2. Measured (red solid line) and simulated (blue dotted line) (a) tidal elevation,
(b) eastward current at 0.62 mab (positive indicates ebbing), (c) northward current at
0.62 mab (negative indicates ebbing), (d) salinity at 1.72 mab, and (e) suspended
sediment concentration at 0.62 mab at site A0.

Figure 3. (a) Measured (red solid line) and simulated (blue dotted line) salinity
profiles at site A0, from left to right it is low slack water, maximum flooding, high
slack water, and maximum ebbing on spring tide, and low slack water, maximum
flooding, high slack water, and maximum ebbing on neap tide. (b) As for (a) but for
suspended sediment concentration.

Figure 4. The left three panels give suspended sediment concentration (unit: kg·m-3)
along the DNC in Case 0 for (a) a daily-average during spring tides, (b) a daily-
average during neap tides, and (c) a monthly-average. Isohalines (unit: psu) are given
in white and zero residual current in black dotted lines. The right three panels give the
along-channel velocity skews of (d) M2 and M4 interaction, (e) M2, S2, and MS4
interaction, and (f) their combination with residual current in Case 0. Note that the
calculation based on equation (D4) and (D5) gives a flood-dominant velocity skew
when γ2(u) >0 or γ3(u) >0. Note that the scales differ. The bottom panel show (g) the
monthly-averaged erosion/deposition rate (unit: kg·m-2s-1, positive for deposition)
along the DNC in Case 0. Channel cells are shown in Figure 1.

Figure 5. The daily-averaged near-bed suspended sediment concentration (contour

lines, unit: kg·m-3) and suspended sediment flux (vectors, unit: kg·m-2s-1) during (a)
spring tides and (b) neap tides in Case 0 in the top panels, and during (c) spring tides
and (d) neap tides in Case 2 in the bottom panels.

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Figure 6. The along-channel near-bottom suspended sediment concentration (unit:
kg·m-3) for (a) Case 0 and (b) Case 6. The white line shows the tidal elevation at site
A0 with leftward indicating high tides.

Figure 7. The left panels give along-channel estuarine gravitational circulation (unit:
ms-1, positive seaward) during (a) spring tides and (b) neap tides in Case 0, and
asymmetric-tidal-mixing-induced flow during (c) spring tides and (d) neap tides in
Case 0, where the white lines indicate 0 ms-1. The right panels show the difference
between Case 0 and Case 1 (Case 0 − Case 1) of along-channel density-driven flow
(unit: ms-1, positive seaward) during (e) spring tides and (f) neap tides, and of
asymmetric-tidal-mixing-induced flow during (g) spring tides and (h) neap tides. For
reference, the white contour lines give the simulated flows in Case 1. Note that the
scales differ.

Figure 8. The suspended sediment concentration (unit: kg·m-3) along the DNC for (a)
a daily-average during spring tides, (b) a daily-average during neap tides, and (c) a
monthly-average in Case 1 in the left panels. The right panels show as for the left
panels but for Case 2. Isohalines (unit: psu) are given in white and zero residual
current in black dotted lines. Note that the scales differ.

Figure 9. The monthly-averaged near-bed suspended sediment concentration (contour

lines, unit: kg·m-3) and suspended sediment flux (vectors, unit: kg·m-2s-1) for (a) Case
0, (b) Case 1, (c) Case 3, (d) Case 4, (e) Case 7, and (f) Case 8.

Figure 10. The monthly-averaged suspended sediment concentration (unit: kg·m-3)

along the DNC for (a) Case 3, (b) Case 4, (c) Case 5, and (d) Case 6. Isohalines (unit:
psu) are given in white and zero residual current in black dotted lines. Note that the
scales differ.

Figure 11. The monthly-averaged vertical diffusivity (Kh, unit: m2s-1, shown as log10
(Kh)) along the DNC in (a) Case 0, (b) Case 1, and (c) Case 5.

Figure 12. The left panels give monthly-averaged maximum bottom orbital velocity
(unit: ms-1) in (a) Case 0, (b) Case 7, and (c) Case 8. The right panels show the

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monthly-averaged significant wave height (unit: m) in (d) Case 0, (e) Case 7, and (f)
Case 8.

Figure 13. The monthly-averaged suspended sediment concentration (unit: kg·m-3)

along the DNC for (a) Case 7 and (b) Case 8 in left panels. Isohalines (unit: psu) are
given in white. The right panels show the monthly-averaged current velocity (unit:
ms-1, positive seaward) along the DNC for (c) Case 7 and (d) Case 8. The white lines
indicate 0 ms-1. Note that the scales differ.

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Table 1. Parameters used in the suspended sediment transport model

Parameter Value Reference

ws0 -8.57×10-6 (ms-1) Tested
m1 -0.006 Tested
n1 2.20 Mehta and McAnally [2008]
m2 1.70 Mehta and McAnally [2008]
n2 2.80 Mehta and McAnally [2008]
C0 0.20 (kg·m-3) Mehta and McAnally [2008]
E0 1.2×10-4 (kg·m-2s-1) Tested
τce 0.8 (kg·m-1s-2) Tested
τcd 0.6 (kg·m-1s-2) Tested
z0b 1.0×10-4 (m) Tested
Table 2. Difference in harmonic constants at eight tide stations (shown in Figure 1) between the
standard model run (Case 0) and measurements

Station Station M2 S2 K1 O1
No. Name Amp(m) Pha(°) Amp(m) Pha(°) Amp(m) Pha(°) Amp(m) Pha(°)
1 DajiShan -0.02 14 0.05 14 -0.01 5 -0.02 4
2 Lvhuashan 0.01 -11 0.00 -6 -0.01 -2 0.01 -4
3 Nanhui 0.00 -5 0.05 3 0.00 1 0.01 2
4 Jiuduansha 0.08 -5 0.05 3 -0.01 -7 0.03 -1
5 Zhongjun 0.00 1 -0.04 10 -0.04 7 0.00 1
6 Wusong -0.02 -3 -0.01 18 -0.02 12 0.01 8
7 Sheshan -0.01 -4 0.03 -8 0.04 -7 0.00 -2
8 Beicao 0.01 -2 -0.01 1 -0.05 8 0.01 2
RMS 0.030 7.0 0.035 9.6 0.028 6.9 0.013 3.2
Table 3. Skill scores (SS) and correlation coefficients (CC) from comparison of model with
observations in 2009

Parameter Skill Score Correlation Coefficient

Tidal elevation 0.951 0.983
Eastward velocity (Bottom) 0.872 0.949
Northward velocity (Bottom) 0.752 0.893
Eastward velocity (Profile) 0.942 0.974
Northward velocity (Profile) 0.907 0.958
Salinity (Bottom) 0.885 0.944
SSC (Bottom) 0.352 0.642
Salinity (Profile, Spring) 0.836 0.942
Salinity (Profile, Neap) 0.848 0.938
SSC (Profile, Spring) 0.342 0.851
SSC (Profile, Neap) 0.301 0.811
Table 4. Summary of case configurationsa and the monthly- and spatial-averaged bed erosion rate and
SSC in each case

Erosion Rate SSC

Case No. Description
(kg·m-2s-1) (kg·m-3)
0 Control run described in Section 2 2.94 1.28
1 Uncoupled SSC and seawater density 5.00 0.84
2 Morphology and bathymetry before the DNC project 3.08 3.23
3 High river discharge in dry season (40,000 m3s-1) 4.43 1.06
4 Low river discharge in dry season (10,000 m3s-1) 4.52 1.82
5 No surface wave-breaking effects 2.23 1.54
6 No bottom wave-current interaction 7.42 0.46
7 Steady northwesterly wind with 10 ms-1 wind speed 0.04 2.35
8 Steady southeasterly wind with 10 ms-1 wind speed 4.35 2.97
a
Cases 1-8 have identical configuration to Case 0, except as described above.