Water Resour Manage (2017) 31:4353–4366
DOI 10.1007/s11269-017-1752-0

Long-Term Quantification of Stream-Aquifer Exchange
in a Variably-Saturated Heterogeneous Environment
V. Phogat 1 & N. J. Potter 2 & J. W. Cox 1,3 & J. Šimůnek 4
Received: 5 May 2016 / Accepted: 12 June 2017 /Published online: 21 June 2017
# Springer Science+Business Media B.V. 2017

Abstract A variably-saturated finite element model HYDRUS-2D was used to simulate thespatiotemporal dynamics of stream-aquifer exchange for a perennial stream flowing through an
undulating catchment and underlain by heterogeneous geology. The model was first calibrated
and validated using piezometric heads measured near the stream. The model was then used a) toquantify the long-term dynamics of exchange at stream-aquifer interface and the water balance inthe domain, and b) to evaluate the impact of anisotropy of geological materials, thickness (w) andhydraulic conductivity (Ks) of the low permeability layer at the streambed, and water tablefluctuations on the extent of exchange. Simulated pressure heads in the domain revealed thatseasonal groundwater fluctuations were more pronounced near the stream. Daily discharge to thestream varied from 0.05 to 0.3 mm/day, annual discharge ranged from 59 to 74 mm, and theoverall water balance showed a discharge (−54 mm) from the domain during 2000–2012. A fivefold increase in Ks of the low permeability layer enhanced discharge to the stream by 14%(10 mm/year) whereas an increase in the thickness of the layer by 1 m had a low impact (2.4 mm/year). A 2-m drawdown of the water table transformed a connected and gaining system into a
The original version of this article was revised: The last page was missing and it contained the below references.
Taylor AR, Lamontagne S, Crosbie R (2013) Measurements of riverbed hydraulic conductivity in a semi-arid
lowland river system (Murray-Darling Basin, Australia). Soil Res 51:363–371
Thompson S (2003) Using Hydrus 2D to model tree belts for salinity and recharge control. Submitted in partial
fulfilment of the requirements of the Degree of Bachelor of Engineering (Environmental) with Honours. Centre
for Water Research, The University of Western Australia, Perth
Xian Y, JinM, Liu Y, Si A (2017) Impact of lateral flow on the transition from connected to disconnected stream–
aquifer systems. J Hydrol 548:353–367* V. Phogat
vinphogat@gmail.com

1

South Australian Research and Development Institute, GPO Box 397, Adelaide SA 5001, Australia

2

CSIRO Land & Water Flagship, GPO Box 1666, Canberra ACT 2601, Australia

3

The University of Adelaide, PMB1, Glen Osmond SA 5064, Australia

4

Department of Environmental Sciences, University of California, Riverside CA 92521, USA4354

Phogat V. et al.

losing, disconnected system. These results suggest that depletion of groundwater due to climatechange or excessive pumping could have a pronounced impact on the availability of water
resources and sustainability of the existing water-dependent ecosystem.
Keywords Stream-aquifer exchange . HYDRUS-2D . Low permeability layer . Anisotropy .
Groundwater

1 Introduction
Exchange between surface water and groundwater (SW-GW) is a complex process, which plays
an important role in the assessment of riparian systems (Sophocleous 2002). Proper quantification of this process helps in decision making about the allocations of water to different users,
including environmental water to preserve the natural ecosystem. SW-GW exchange depends
on many factors, including topography, subsurface hydraulic properties, climate, and vegetation(Banks et al. 2011). The exchange of water has a controlling influence on the stream chemistry,
nutrient fluxes, near stream biota, and biogeochemical conditions in the vicinity of the creek andcreek flow during dry periods (Frei et al. 2009). To better understand the nature of interactions
between groundwater and stream requires reliable estimation of the flux across the stream.
There are numerous measurement techniques and approaches for quantification of flow
between stream and groundwater (e.g. Kalbus et al. 2006; Chu et al. 2017). However, in mostcases, a limited number of data points results in the lack of detailed understanding ofgroundwater-surface water interactions which hinders the evaluation of continuous flow withina spatiotemporal domain. Numerical modelling approaches, on the other hand, can be valuable
tools for developing a better understanding of the system by combining information obtained
from various field methods. Once a model is accurately conceptualized, sufficiently calibrated
and validated, it can be used to quantify water fluxes and water balance, and to predict their
spatiotemporal changes under different scenarios.
Many reviews have summarized the empirical, analytical and process-based numericalsolutions employed to understand the complex nature of SW-GW flow systems at different
scales (e.g. Barthel and Banzhaf 2016; Chu et al. 2017). Nevertheless, the major complexity inthe use of these models is the requirement of spatiotemporal input data for climate, vegetation,
stream-flow, groundwater fluctuations, and heterogeneous geological formations. In addition
to this, calibration and validation of process based models under such situations also poses
enormous challenges. Numerous physically based SW-GW coupled modelling tools (e.g.
Guzman et al. 2015) have been used over different scales which often undermine the impact
of near stream water dynamics, temporal and spatial hydrological and geological heterogeneity, and anisotropy on SW-GW exchange. Banks et al. (2011) evaluated the importance ofvegetation on the nature of the connection between SW-GW and conceptualized the impact ofa clogging layer (a low hydraulic permeability layer at the bed), evapotranspiration, and theslope of the catchment using the 2-D HydroGeoSphere model, assuming both homogeneousand isotropic conditions. Batlle-Aguilar et al. (2015) calibrated and validated a 2D model foran ephemeral stream assuming isotropic and no flow conditions at the soil surface. Similarly,
Xian et al. (2017) analyzed the importance of lateral flow on SW-GW using conceptual
transient simulations for the 2D and 3D systems in the context of heterogeneous streambeds.
The importance of heterogeneities at the stream-groundwater interface and in the hyporheic
zone on the exchange has been emphasized in many short-term conceptual studies (e.g. Frei

Long-Term Quantification of Stream-Aquifer Exchange

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et al. 2009). Meanwhile, Doble et al. (2012) evaluated the overbank flood recharge using a
numerical model and found that an increase in the conductance of the clogging layer at theriverbed increased the infiltration volume. Similarly, infiltration rates from a losing, disconnected river obtained from measurements and modelling studies were found to be moresensitive to the clay layer hydraulic conductivity than to its thickness (Crosbie et al. 2014).
Normally, the estimation of SW-GW interactions in these studies (e.g. Doble et al. 2012;
Crosbie et al. 2014; Rivière et al. 2014) has been conducted assuming either homogeneous andisotropic conditions, or groundwater normal to the stream. However, biophysical modellingstudies, with models calibrated and validated on data from sites involving multiplehydrogeological heterogeneities, such as anisotropic flow and/or the presence of poorly
permeable layers, are scarce. It is thus essential to develop long-term detailed knowledge on
SW-GW interactions based on proper calibration and validation of a numerical model considering vegetation, geology and the permeability of the streambed in the vicinity of the stream inorder to derive quantitative information about the system.
This study uses a finite element two-dimensional numerical model (HYDRUS-2D;Šimůnek et al. 2016) to quantify the extent of stream-aquifer connectivity involving realtime climatic, vegetative, and stream flow conditions under complex heterogeneous geologicalformations. The objectives of the study were i) to calibrate and validate HYDRUS-2D for
spatiotemporal dynamics in the piezometric heads at multiple locations in the vicinity of a
stream, ii) to quantify the long-term exchange between stream and groundwater and to estimate
the overall water balance in the 2D domain, and iii) to evaluate the impact of thickness andconductivity of a low permeable layer at the streambed, anisotropy of geological materials andthe depletion of the water table on the extent of exchange between stream and groundwater.

2 Material and Methods
2.1 Site Description
The study site is located at Scott Bottom (35° 06′ S and 138° 40′ E) in Scott Creek, in the
Mount Lofty Ranges of South Australia. The study site comprises of natural vegetation mostly
dominated by the Eucalyptus species. The soils at Scott Bottom are duplex (Chittleborough1992), that is 0.3–0.5 m of light-textured sandy loam overlays heavy-textured clay. The soil isunderlain by saprolite (1.3–2.4 m to 6–18 m) and then fractured rock (Banks et al. 2009). The
climate at the site is Mediterranean with warm dry summers and cool wet winters. The Scott
Bottom gauging station (SA Water) has rainfall and run off records from 1991 until present,with mean and median annual rainfall of 804 and 764 mm/year, respectively. The gauging
station also measures daily stream flow and the water level in the creek at Scott Bottom whichwere used in the present investigation. Details on the drilling, installation, measurements andmonitoring of piezometric wells are described in previous studies (James-Smith andHarrington 2002; Harrington 2004; Banks et al. 2009).

2.2 Numerical Modelling
Temporal and spatial movement of water in a two-dimensional transport domain (Fig. 1) was
simulated using HYDRUS (2D/3D), version 2.xx (Šimůnek et al. 2016) which has been
widely used in both vadose zone and groundwater studies. The governing two-dimensional

4356

Phogat V. et al.

water flow equation is described by a modified form of the Richards equation which assumes
that the air phase plays an insignificant role in the liquid flow process and that water flow dueto thermal gradients can be neglected:




∂θ
∂
∂h
∂
∂h
¼
K ðhÞ
K ðhÞ þ K ðhÞ −S ðhÞ
þ
∂t
∂x
∂x
∂z
∂z

ð1Þ

where θ is the soil water content [L3 L−3]; t is time [T]; h is the pressure head [L]; x is the horizontal
coordinate; z is the vertical coordinate (positive upwards); K(h) is the hydraulic conductivity[LT−1], and S(h) is the sink term representing root water uptake [T−1]. Water extraction S(h) was
computed according to the Feddes model (Feddes et al. 1978). Feddes parameters for native
vegetation (Eucalyptus species) were taken from Thompson (2003), optimized for Australianconditions. Readers are referred to the HYDRUS web site (http://www.pc-progress.
com/en/default.aspx) for more details about the software and its applications.

2.3 Modelling Domain
The modelling domain (Fig. 1) represents the creek at Scott Bottom which was 335 m wide
(x = 0 at the left boundary, positive in the right direction) and 42 and 56 m deep (z, positive
upwards) on the western and eastern sides of the creek, respectively. The creek is located at
x = 135 m and is represented by a bed width of 2.5 m, a top width of 5 m, and a depth of 4 m(Banks et al. 2009). The colours in Fig. 1 differentiate the complex geology including soil,
saprolite and fracture rock. Fig.1 also shows the location of piezometers and boundary conditions.
The domain was discretized into 44,171 triangular elements with a fine grid around the creek(0.2 m) and along the sides with time-variable pressure head boundary conditions. The grid size
was gradually increased farther from these locations with a maximum element size of 1 m.

2.4 Soil Hydraulic Parameters for Modelling
Retention parameters of duplex soils were obtained from ROSETTA embedded in HYDRUS-2D
and Ks values were obtained from Banks et al. (2009). Similar hydraulic conductivities of A and B

Fig. 1 A schematic (stretched in the vertical direction) of the model domain showing material distribution,boundary conditions, the initial position of the water table, and the location of piezometers

Long-Term Quantification of Stream-Aquifer Exchange

4357

horizons of the soil were reported by Cox and Pitman (2002) in the Mount Lofty Ranges of South
Australia. The hydraulic conductivities of the saprolite and fractured rock layers were crucial for
simulating flow to the creek while maintaining the elevation heads measured at nested piezometers. Flow in a fractured rock depends on the relative proportion and properties of the fracture andmatrix systems, such as the size, conductivity, tortuosity of fractures, and porosity and conductivity of the matrix which makes it hard to model (Šimůnek et al. 2003). Although dual-porosityand dual-permeability models exist for such complex environments, the difficulty in determining
many dual-permeability model parameters largely limits the applicability of these models (Köhne
et al. 2009). Hence, the modelling of the fractured rock system was simplified by assuming it to be
represented by a single-porosity material.
Since the geology of the site is dominated by sandstone, siltstone and dolomite, the saturated
water content for fractured rock was considered to be 20% (Leaney et al. 2011) and the shapeparameter α was taken from Banks et al. (2011). Banks et al. (2009) reported a wide range of Ks
values measured using single well aquifer tests for saprolite (0.04–2.5 m/day) and fractured
rock (1.5–14 m/day) at locations near Scott Creek. In order to realistically represent the flow
conditions at the site, the soil hydraulic parameters were calibrated against the piezometricwater level fluctuations and a sensitivity analysis was performed for the hydraulic conductivityof saprolite and fractured rock. Final van Genuchten parameters used in the model are shown in
Table 1. Note that parameters θr, α, n, and l are not needed for layers that are fully saturated.

2.5 Estimation of Potential Transpiration, Evaporation and Root Distribution
Daily potential evapotranspiration (PET) for natural tree (Eucalyptus) vegetation for theexperimental site were obtained from the SILO database (Jeffrey et al. 2001). The data wereconverted to potential transpiration (Tp) and potential evaporation (Es) based on the leaf areaindex and rainfall correlation developed by Ellis and Hatton (2008) for South Australiancatchments under natural Eucalyptus vegetation. The daily PET values were split into Tp andEs as follows (Belmans et al. 1982):
E s ¼ PET ⋅e−K gr LAI

ð2ÞT p ¼ PET −E s
Here, Kgr is the light extinction coefficient for global solar radiation and its value was taken
as 0.5 for forest systems (Aubin et al. 2000). Estimated Es and Tp values were used as input for
HYDRUS-2D simulations.

Table 1 Calibrated soil hydraulic parameters of different materials used in the model
Material
Sandy loam
Silty clay loam
Saprolite
Fractured rockLow permeability layer*θr (m3 m−3)*

θs (m3 m−3)*α (m−1)*n*

Ks (m day−1)

*

0.06
0.06
0.06
0.06
0.06

0.41
0.41
0.35
0.26
0.41

4
2
2.2
4
1.9

1.89
1.35
1.4
1.9
1.31

1.05
0.05
0.5
0.03
0.05

0.5
0.5
0.5
0.5
0.5

l

θr is the residual water content (L3 L−3 ), θs is the saturated water content (L3 L−3 ), Ks is the saturated hydraulicconductivity (LT−1 ), l is a shape factor, α is an inverse of the air-entry value and n is an empirical parameter

*

4358

Phogat V. et al.

Rooting depth of Eucalyptus trees was obtained from the literature (Canadell et al.
1996). Since imposing an exact rooting depth along the hill slope was difficult, thesimulated rooting depth varied between 6 and 7 m. The root water uptake distribution
was assumed to be linearly distributed with depth between a maximum at the top andzero at the bottom.

2.6 Initial and Boundary Conditions and Model Calibration
The initial pressure head condition in the domain was specified by interpolating measured
mean piezometric elevation heads (of nested piezometers) while considering hydrostatic
equilibrium from the lowest located nodal point. The seepage face boundary condition
specified in the creek was coupled with special boundary condition options allowing for theinterpolation of variable pressure heads in time and imposing the seepage face boundary
condition when the specified nodal pressure head was negative. Hence, the specified waterlevels in the creek were linearly interpolated in time, in order to smooth the impact of daily
fluctuations of water levels in the stream. Measured values at nested piezometers A and F(Fig. 1) were used to define time-variable pressure head boundary conditions at the sideboundaries. This initial pressure head condition at side boundaries was further optimized
during calibration so that it maintains the piezometric head fluctuation close to the measured
level in the nested piezometers in space and time. The bottom boundary was assumed to be a
Bno flow^ boundary. The atmospheric boundary condition was imposed at the surface where
rainfall, evaporation, and transpiration changes over time. Since HYDRUS cannot reliably
simulate overland flow on slopes, rainfall minus run off was assumed to instantaneously
infiltrate into the soil.
Simulations were carried out for 535 days from 15th July 2005 till 31st December
2006 to calibrate the model by comparing the measured and modelled spatiotemporal
piezometric heads at four locations (B, C, D, and E) shown in Fig. 1. The model wascalibrated via a trial-and-error manipulation of hydraulic parameters and validated for365 days from 1st January 2007 till 31st December 2007. The model was then employed
to assess the long-term (2000 to 2012) dynamics of SW-GW connectivity in the creek at
Scott Bottom under Eucalyptus (trees) vegetation by employing measured daily waterlevel and climate parameters.

2.7 Impact of a Low Permeability Layer, Anisotropy and Water Table Drawdown
The calibrated model was run for different Kh/Kv ratios (0.75, 1, 1.5, 2.0, 2.5, 3.0) of soil,
saprolite and fractured rock zone to evaluate the impact of anisotropy on the extent ofdischarge to the creek. Similarly, the impact of the low permeability layer at the bottom of
the stream was evaluated by considering five thicknesses (0.00 m, 0.25 m, 0.50 m, 0.75 m and1.00 m) and four hydraulic conductivities (Ks = 0.02, 0.05, 0.075 and 0.1 m/day) of thestreambed. These characteristics were selected on the basis of field studies of the thickness andhydraulic conductivity measurements of the low permeability layers in the Murray Darling
Basin (Taylor et al. 2013). Scenarios with different levels of water table drawdown (0.25, 0.5,
0.75, 1.0, and 2.0 m) along the slope of the domain were performed to evaluate the impact on
the state of connection between the stream and aquifer system. These scenarios were developed as a result of declining trends in groundwater levels (0.02–1.7 m/year) in 71% of theobservation wells over the five years (2010–2015) in the study area (DEWNR 2016).

Long-Term Quantification of Stream-Aquifer Exchange4359

3 Results and Discussion
3.1 Comparison of Pressure Heads

RSWL (mAHD)RSWL (mAHD)

The measured piezometric heads at four nested sites (Banks et al. 2009), situated at
x = 125 (E), 160 (D), 190 (C), and 260 m (B) from the left side of the domain (Fig. 1)
are compared in Fig. 2 with corresponding heads generated by HYDRUS-2D during thecalibration (from 15th July 2005 to 31st December 2006) and validation (from 1st
January 2007 to 31st December 2007) periods (900 days). While there was a good
temporal match between simulated and measured pressure heads at 3 locations (C, D, andE), the model simulated lower heads at x = 260 m (B). Here, both measured andsimulated values showed much smaller seasonal response and modelled pressure heads
were lower than measured values. Simulated seasonal amplitude in pressure heads also
matched well with water table fluctuations in piezometers at locations D and E.
However, the simulated seasonal response at location C was low compared to measured
values. The results revealed that seasonal variations in the pressure heads are enhancednear the creek and gradually dissipate away from the creek (Fig. 2).
Differences between modelled and measured values, particularly at location B, may be due
to localized hydrogeological heterogeneity. This cannot be captured by the model simulations,since the flow patterns in the fractured rock are highly sensitive to the size, shape, andconnectivity of fractures, as well as to matrix properties. Nevertheless, modelled variabilityof heads near the creek (i.e., at locations D and E) showed much higher correspondence withmeasured values and these locations are likely to have a much greater effect on surfacegroundwater exchanges at the creek. In contrast, Batlle-Aguilar et al. (2015) observed thatmatching measured and simulated piezometric heads under ephemeral streams and for disconnected stream-aquifer interface (Lamontagne et al. 2014) does not imply that a model
simulates stream infiltration well in all situations. They reported that groundwater mounding
can affect the model simulations which is normally absent under gaining system as observed in
the present study.

208

208

207

207

206

206

205
204
203

B4
B5
Sim

205

C4
C5
Sim

204
203

202
202
17/02/05 5/09/05 24/03/06 10/10/06 28/04/07 14/11/07 1/06/08 17/02/05 5/09/05 24/03/06 10/10/06 28/04/07 14/11/07 1/06/08
208
208
E1
E2
E3
E4
D1
D2
D3
D4
D5
207
207
E5
E6
Sim
D6
D7
D8
Sim
206
206
205
205
204

204

203

203

202
202
17/02/05 5/09/05 24/03/06 10/10/06 28/04/07 14/11/07 1/06/08 17/02/05 5/09/05 24/03/06 10/10/06 28/04/07 14/11/07 1/06/08
Date
Date

Fig. 2 Comparison of measured and simulated RSWLs (reduced standing water levels) during calibration (15thJuly 2005 to 31st December 2006) and validation (1st January 2007 to 31st December 2007) at 4 locations (B, C,
D, and E). AHD is the Australian height datum

4360

Phogat V. et al.

3.2 Long-Term Discharge to the Creek and Annual Water Balance

Daily discharge (mm)

(a)

0.35

0

0.28

20

0.21

40

0.14

60

0.07

80

0

100

Rainfall (mm)Simulated long-term (2000 to 2012) daily discharge to creek at Scott Bottom showed a distinct
annual pattern of flow over the years influenced by the amount of rainfall and the hydrologicalflux exchange within the domain (Fig. 3a). The impact of low rainfall during 2007 to 2009 isclearly visible on the daily magnitude of discharges to the creek. Low rainfall not only reduced
the magnitude of flow in the creek but also the amount of discharge to the creek. Daily discharge
to the creek varied from 0.05 to 0.31 mm/day. Normally, high intra-annual discharges occurred
during September–October and low during April–May. Since the rainfall season usually occurs
from June to August, this indicates that the impact of rainfall on water movement to the creek is
not immediate but it has a lag time depending upon the rainfall amount, intensity, and geology
since recharge flows through complex geological pathways, as speculated by Banks et al.
(2009). Baseflow conditions (between 0.05–0.1 mm/day) in the Scott Creek typically occurred
during February to May period (Fig. 3a). Annual discharge to the creek varied from 58.9 to
73.8 mm and the impact of low rainfall was observed during 2006–2008.
These results (positive discharge to the creek) also confirm that the Scott creek at Scott
Bottom is a gaining creek which corroborates with other studies (James-Smith and Harrington
2002; Banks et al. 2009). However, these studies could not quantify the contribution of lateralgroundwater flow to the creek. Our calibrated and validated model showed that most lateralflow (83–86%, Fig. 3b) to the creek was contributed from the left side of the domain at
piezometer F (see Fig. 1) due to the continuously higher groundwater table level, and acorrespondingly higher vertical hydraulic gradient, than from a comparatively constantgroundwater level and a low gradient at the right side of the domain at piezometer A.

Date

Boundary flux (mm)

(b)
-100
-80
-60
-40

A

F

-20
0

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
Years

Fig. 3 Long-term daily dynamics in a) discharge to the creek and rainfall, and b) simulated annual boundary
fluxes through the A and F piezometer (see Fig. 1) boundaries of the flow domain

Long-Term Quantification of Stream-Aquifer Exchange

4361

The model-simulated annual ET losses for native trees (Eucalyptus species) varied from 698 to
832 mm, while the mean annual ET losses over a period of 13 years amounted to 772 mm (Fig. 4a).
Despite low precipitations during 2006, the annual ET losses were maintained near mean value.
This implies that the ET demand was continuously met and the groundwater table depths were also
remained at the same level due to continuous replenishment by lateral groundwater flow towards
the stream. However, the impact of low rainfall during 2006 and 2007 was visible during 2008 as
the ET losses reduced to a great extent but maintained at a higher level than annual rainfall. Actual
ET under natural Eucalyptus vegetation can often exceed precipitation (Sun et al. 2011) which canstrongly influence the connectivity of losing streams in dry years (Banks et al. 2011).
On the other hand, water balance estimation showed an overall positive balance (i.e.
groundwater recharge condition) in the domain under Eucalyptus trees during 2001, 2003,
2005, 2007–2010 (Fig. 4b). However, in the remaining years, an overall negative balanceprevailed. The maximum annual discharge from groundwater storage (−151.6 mm) was
observed during 2006, when the region experienced severe low rainfall conditions. Overallwater balance over the study period (2000–2012) showed a discharge of 54 mm from thedomain. This discharge has not been replenished at Scott Bottom by lateral or regional flows,which feed the creek system. Similar observations were made by Ivkovic et al. (2009) in the
Cox Creek catchment where groundwater discharge was observed. Nevertheless, discharge/
recharge conditions at Scott Bottom are affected by a number of interrelated factors: a) theexperimental site has a shallow water table along the creek, which is being replenished with
regional flow due to a gaining stream system; b) the roots of Eucalyptus trees extend to a depthof more than 5 m, drawing water from both the vadose zone and groundwater; c) highevapotranspiration demand under the semi-arid conditions of the catchment; and d) relatively
less rainfall during the study period. This type of situation generally exists in areas where theevapotranspiration demand is very high in comparison to precipitation and an easy access toshallow groundwater is maintained by deep rooted vegetation along the stream (Landmeyer2012). Under shallow water table conditions and deep rooted systems, it is mainly vegetationthat controls groundwater recharge, as observed in this study. Groundwater discharge conditions have also been reported in other studies (Ordens et al. 2014) involving deep rooted
Mallee trees (Eucalyptus species), similar to those in the Scott Creek catchment. In contrast,
other studies (e.g., Green and Zulfic 2008) reported groundwater recharge ranging from 16 to
111 mm/year in various catchments of South Australia. Such dramatic contrasts often exist

(b)

(a)

Annual recharge/discharge (mm)850

Annual ET (mm)

800
750
700
650
600
550
500

150
100
50
0
-50

-100
-150
-200
2000

2002

2004

2006 2008
Years

2010

2012

Years

Fig. 4 Model-simulated a) annual evapotranspiration (ET) of native vegetation (Eucalyptus species) and b) the
annual water balance in the domain at Scott Bottom during 2000–2012

4362

Phogat V. et al.

when there is a huge variation in methodology, and different sites, climate, topography,
vegetation, and other parameters needed for recharge estimation.
The results also reveal that vegetation plays an active role in affecting the stream flow andthe nature of the hydraulic connection between SW-GW through its influence on water
extraction patterns from the soil. This impact varies depending on evapotranspiration,reflecting different climates, leaf areas, root systems, and different stress response mechanisms.
Numerous studies (e.g. Leaney et al. 2011; Ordens et al. 2014) have shown a pronounced
impact of vegetation on recharge to groundwater and on surface-subsurface hydrologicalinteractions (Li et al. 2013). Undoubtedly, the ET losses due to vegetation drive the natureof the connection between SW-GW.

3.3 Impact of Low Permeability Layer, Anisotropy and Water Table Dynamics
Discharge to the creek increased nonlinearly with an increase in the hydraulic conductivity(Ks) of the layer (0.5 m width) at the streambed (Fig. 5a). An initial increase of Ks from 0.02 m/
day to 0.05 m/day produced a 9.4-mm increase in discharge to the creek. However, further
increases in Ks from 0.05 m/day to 0.075 and to 0.1 m/day resulted in diminishing increases indischarge to the creek (2.4 and 1.4 mm, respectively). Hence, decreasing Ks of the streambed
layer from 0.1 m/day to 0.02 m/day resulted in a 14% (10 mm/year) reduction in the amount ofdischarge to the creek. On the other hand, increasing the thickness of the streambed layer (w)to 1 m had a relatively much smaller impact on discharge to the creek (reduced discharge tostream by 3%; Fig. 5b). Hence, the relative impact of Ks of the streambed layer as compared to
its thickness w was four times larger, indicating the crucial role of Ks of the streambed of againing system. In contrast, the impact of anisotropy of saprolite was much higher than that of
the fractured rock and soil zone (data not shown). For the anisotropy ratio of 3 for saprolite, thecreek discharge almost doubled, which is quite significant. This happens because the watertable is situated within the saprolite zone and lateral flow towards the creek is highly
influenced by the hydraulic properties of this zone. Frei et al. (2009) showed that spatial andDischarge to creek (mm)

100

(a)

100

95

95

90

90

85

85

80

80

75
80

0.02
0.05
0.075
0.1
Hydraulic conductivity (m/day)

75

(b)

0

(c)

0.25
0.5
0.75
Layer thickness (m)

1

60
40
20
0
-20
-40

0.0 m

0.25m

0.5m
0.75m
Water table drawdown (m)

1.0m

2.0m

Fig. 5 Changes in the discharge to the creek in relation to a) the hydraulic conductivity (Ks), b) the thickness of
the low-permeability layer (w), and c) the water table depletion at Scott Bottom from 15th July 2005 till 31st
December 2006

Long-Term Quantification of Stream-Aquifer Exchange

4363

Daily discharge to creek (mm)temporal heterogeneity can cause distinct patterns of dynamics of river seepage in an alluvial
aquifer overlying a deep water table and most seepage occurs along preferential flow zones.
Nevertheless, these preferential flow paths are difficult to consider in numerical simulations.
The water table decline has a pronounced effect on stream discharge, which continues todecrease linearly with the decrease in the depth to water table (Fig. 5c). Discharge decreased to18.4 mm with a 1.0-m drop in the water table during the period from 15th July 2005 to 31st
December 2006 (535 days). This decrease in discharge is equal to about one-third of discharge
under existing conditions. However, detailed simulations of daily values showed that the initiallosing state (Fig. 6) at the stream interface was quickly transformed to a discharge state as longas the water table decrease was less than 1 m. This condition resembles the losing-connected
stream, as described by Lamontagne et al. (2014). In this situation, the water table is quickly
raised near the river by increased infiltration rates, because of a large hydraulic gradient(Rivière et al. 2014). However, a 2.0-m drawdown from the original position produced
persistent losing conditions for much longer time (400 days, Fig. 6) as compared to otherscenarios. This condition seems to resemble losing-disconnected rivers defined by
Lamontagne et al. (2014). Hence, regaining connection or the discharge state does not occur
quickly as the infiltration rate is already at its maximal under losing-disconnected rivers(Brunner et al. 2009) and a compensating effect cannot occur rapidly when the regional watertable falls. However, the situation (disconnection to connection) here is different from mostother conceptual modelling studies (Brunner et al. 2009; Rivière et al. 2014) where flow
processes from connection to disconnection of the stream-aquifer are discussed for homogeneous and isotropic conditions. Under natural conditions with complex hydrological heterogeneity and with water table along the slope, flow processes may react quite differently thanreported in these studies. Therefore, the process of connection and disconnection seems todepend on site-specific hydrogeological, vegetation, climatic, and aquifer conditions; while
treatment and management strategies are thus vary site specific as well.
These results suggest that seasonal water table fluctuations created by low rainfall or
groundwater pumping may have a profound impact on the state of the connection between
the stream and groundwater. The most crucial impact may be inflicted to the survival of theflora and fauna along the creek that is dependent on the stream flow system for their existence.
Future climate change (Beecham 2015) in southern Australia is likely to produce considerable
changes in volumes and intensities of rainfall and may have a tremendous impact on thehydrological state of connection in the Scott Creek.
0.2
0.1
0
-0.1
-0.2
-0.3

0.0 m
0.5 m
1.0 m

0.25 m0.75 m2.0 m

Date

Fig. 6 Simulated daily discharge to the creek at Scott Bottom in relation to the indicated water table depletions at
Scott Bottom from 15th July 2005 till 31st December 2006

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Phogat V. et al.

4 Conclusions
Reliable long-term quantification of discharge fluxes at a stream-aquifer interface is required forthe sustainable management of water resources at local and regional level. This study revealed
that deep-rooted vegetation and site specific geological heterogeneity play a key role on thenature of hydraulic connection and water-flow patterns at the stream-groundwater interface. The
outcomes suggest that when water tables are shallow, deep-rooted vegetation maintains higher
ET losses for a longer time even during low rainfall periods due to continuous lateral inflow
from elevated groundwater zones in the lateral directions. The calibrated and validated model
quantified lateral groundwater flow, which maintained the perennial nature of the creek at Scott
Bottom even during the drought period. Nevertheless, the overall water balance over 13 years
showed more often discharge conditions than recharge under Eucalyptus trees. It was highly
influenced by precipitation coupled with other hydraulic fluxes like lateral flow and ET losses.
It is well known that uncontrolled pumping, depletion of groundwater resources due to land
use change, or climate change could have a serious impact on the amount of discharge to a
stream. This study showed that a groundwater drawdown of 2 m at Scott Creek could lead to asignificant reduction in stream discharge. Gaining systems can quickly become losing systems,
which transforms a perennial stream to a seasonal or ephemeral stream. However, a considerable drop in the water table is required before a connected system transitions into a
disconnected system. This can have serious implications on the sustainability of ecosystem
and a pronounced impact on the management of water resources.
Acknowledgments We acknowledge the financial support provided by the Goyder Institute for Water Research
for this study. We thank Dr. Eddy Banks, Flinders University and Dr. Graham Green, SA Department ofEnvironment Water and Natural Resources for their technical support. The leaves granted to Dr. Vinod Phogat
by CCS Haryana Agricultural University (India) for availing Post-Doctoral studies are highly acknowledged.

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