Investigation of the groundwater modelling component of the Integrated Water Flow Model (IWFM)

ABSTRACT

The Integrated Water Flow Model (IWFM), developed by the California Department of Water Resources, is an integrated hydrological model that simulates key flow processes including groundwater flows, streamflow, stream–aquifer interactions, rainfall–runoff and infiltration. It also simulates the agricultural water demand as a function of soil, crop and climatic characteristics, as well as irrigation practices, and allows the user to meet these demands through pumping and stream diversions. This study investigates the modelling performance of the groundwater module of IWFM using several hypothetical test problems that cover a wide range of settings and boundary conditions, by comparing the simulation results with analytical solutions, field and laboratory observations, or with results from MODFLOW outputs. The comparisons demonstrate that IWFM is capable of simulating various hydrological processes reliably.

EDITOR M.C. Acreman; ASSOCIATE EDITOR A. Efstratiadis     

Hydrogeological characterization of groundwater storage and drainage in an alpine karst aquifer (the Kanin massif,Julian Alps)

The Kanin massif is an important trans‐boundary aquifer, which stretches between Slovenia and Italy. The groundwater is only partially exploited, mainly for water supply, but the aquifer exhibits great potential for future exploitation. Since no consistent regional overview of the hydrogeological functioning of the Kanin massif was available, the decision was made to perform a study of this area, using a pragmatic approach based on 3D geological and hydrogeological modelling. The so‐called KARSYS approach was applied, with the aim of characterizing the groundwater reserves within this karst massif and of locating the main drainage axes that carry groundwater from the recharge areas to the respective springs. Delineation of the catchment areas of the corresponding springs was carried out, and some new explanations were obtained, especially with regard to the Mo?nica spring, which is located in Slovenia and forms a potential source of drinking water. It was found that this spring's catchment area extends as far as the Italian ski resort of Sella Nevea. The conceptual model also provides a possible explanation about the underground drainage towards the Boka spring and waterfall, which has been a challenge for decades. This new explanation is based on the existence of a perched groundwater body that feeds the Boka spring via a system of conduits. Despite some limitations, the results, which consist of a visualization of the underground drainage and groundwater storage within the Kanin massif, can be used as a basis for planning the sustainable management of karst waters in the studied area. Copyright © 2014 John Wiley & Sons, Ltd.     

Simulated groundwater interaction with rivers and springs in the Heihe river basin

Surface water and groundwater in the Heihe river basin of China are interconnected and the pattern of water resources exploitation has a direct effect on the interaction of groundwater and surface water, especially on a downstream oasis. A three‐dimensional groundwater flow simulation model with eight model layers was established to simulate the regional groundwater flow in the multilayered aquifer system and the interaction among the rivers, springs, and groundwater. The model was calibrated not only with historical water levels but also with the investigated baseflow and spring flux. The simulation results of the numerical model match reasonably well with the observed groundwater levels, baseflow to rivers, and spring flux. The numerical simulation also demonstrates that the hydraulic connection between the river and the aquifers has transferred from the coupling to decoupling at some reaches. It is suggested that there is a vital need to reduce groundwater withdrawal and to rationalize the use of both groundwater and surface water in order to maintain sustainable development in the study area. Copyright © 2007 John Wiley & Sons, Ltd.     

A study of the three-dimensional groundwater flow system in an upland area of Japan

A three-dimensional finite difference model was developed to study the groundwater flow system in an upland area bordering a lake. For a general perspective of the groundwater flow system, a steady state three-dimensional flow was employed. Having determined the flow net by using a three-dimensional model, the flow volumes under natural conditions have been used to establish the parameter values and for the analyses of flow patterns. Further, to study the effects of human impact and precipitation on groundwater flow conditions in a small area, a transient three-dimensional simulation was performed. Environmental tritium was used to trace the regional groundwater movement to verify the three-dimensional mathematical model. Results obtained using the three-dimensional mathematical model approach and tritium concentration analyses were in close agreement. The results demonstrated that the groundwater flow system should be analysed using a three-dimensional geometric concept of groundwater movement.     

Evaluation of the soil water balance in an alluvial flood plain with a shallow groundwater table

Abstract

Many of the hydrological and ecological functions of alluvial flood plains within watersheds depend on the water flow exchanges between the vadoze soil zone and the shallow groundwater. The water balance of the soil in the flood plain is investigated, in order to evaluate the main hydrological processes that underlie the temporal dynamics of soil moisture and groundwater levels. The soil moisture and the groundwater level in the flood plain were monitored continuously for a three-year period. These data were integrated with the results derived from applying a physically-based numerical model which simulated the variably-saturated vertical water flow in the soil. The analysis indicated that the simultaneous processes of lateral groundwater flow and the vertical recharge from the unsaturated zone caused the observed water table fluctuations. The importance of these flows in determining the rises in the water table varied, depending on soil moisture and groundwater depth before precipitation. The monitoring period included two hydrological years (September 2009–September 2011). About 13% of the precipitation vertically recharged the groundwater in the first year and about 50% in the second. The difference in the two recharge coefficients was in part due to the lower groundwater levels in the recharge season of the first hydrological year, compared to those observed in the second. In the latter year, the shallow groundwater increased the soil moisture in the unsaturated zone due to capillary rise, and so the mean hydraulic conductivity of the unsaturated soil was high. This moisture state of soil favoured a more efficient conversion of infiltrated precipitation into vertical groundwater recharge. The results show that groundwater dynamics in the flood plain are an important source of temporal variability in soil moisture and vertical recharge processes, and this variability must be properly taken into account when the water balance is investigated in shallow groundwater environments.

Citation Pirastru, M. and Niedda, M., 2013. Evaluation of the soil water balance in an alluvial flood plain with a shallow groundwater table. Hydrological Sciences Journal, 58 (4), 898–911.     

Use of a watershed hydrologic model to estimate interbasin groundwater flow in a Costa Rican rainforest

The watershed hydrologic model TOPMODEL was used to estimate interbasin groundwater flow (IGF) into a small lowland rainforest watershed in Costa Rica. IGF is a common hydrological process but often difficult to quantify. Four‐year simulations (2006–2009) using three different model approaches gave estimates of IGF that were very similar to each other (10.1, 10.2, and 9.8 m/year) and to an earlier estimate (10.0 m/year) based on 1998–2002 data from a budget study that did not use a hydrologic simulation model, providing confidence in the new estimates and suggesting each of the three model approaches is viable. Results show no significant temporal variation in IGF during 2006–2009 (or between this period and the earlier study from 1998–2002). Simulations of the 16 consecutive 3‐month periods in 2006–2009 gave 16 values of IGF rate with a mean (10.1 m/year, standard deviation = 0.6 m/year) very similar to the estimates above from the 4‐year simulations. This suggests the modified version of TOPMODEL can be used to model stream discharge and estimate IGF for sub‐annual time periods during which change in water storage is not necessarily equal to zero. Thus, simple watershed models may be used to estimate IGF based on even relatively short calibration periods, making such models useful tools in the study of this widespread hydrological process that affects water and chemical fluxes and budgets but is often difficult and costly to quantify. Copyright © 2013 John Wiley & Sons, Ltd.     

Direct observation of complex Tóthian groundwater flow systems in the laboratory

Based on the theory of gravity‐driven groundwater flow systems, we have developed a complex Flow System Sand‐Box Model (FSM). It enables the visual observations of the development and characteristics and temporal evolution of complex Tóthian flow systems in the laboratory. The configuration of the regional, intermediate and local flow systems can be controlled and observed; hydraulic head, flow direction and travel time can be measured; and the scale and shape of the sub‐flow systems as well as the path lines and flow lines can be observed directly. The experiments demonstrate the Tóthian flow systems in a small basin with multiple sources and sinks. Greater local topographic (water table) undulation will lead to larger local flow systems. Greater regional and less local topographic undulation will enhance the development of intermediate and regional flow systems. In homogeneous media, increasing fluid‐potential differences between source and sink increase the spatial scale of the generated flow systems. The FSM is a useful teaching aid and experimental device to study and develop an intuitive insight into gravity‐driven groundwater flow systems. It helps to visualize and understand the hydraulic properties and controlling factors of Tóthian flow systems and may be used to study problems related to the chemical and temperature characteristics of the flow systems as well. Copyright © 2010 John Wiley & Sons, Ltd.     

Unraveling the roles of asymmetric uplift,normal faulting and groundwater flow to drainage rearrangement in an emerging karstic landscape

Landscape adjustment to tectonic, lithologic and climatic forcing leads to drainage reorganization and migration of divides. The respective contribution of these forcings, especially on carbonate landscapes is not well defined. Here, we have addressed this issue by combining field observations, satellite image interpretation and digital elevation model (DEM) quantitative analysis to assess drainage response to spatially heterogeneous rainfall, asymmetric uplift, and normal faulting on an emerging carbonated platform (Sumba Island, Indonesia). We map geomorphic markers of fluvial dynamics and drainage rearrangement and compute a χ parameter that incorporates the contributions of unevenly distributed precipitation and asymmetric uplift to estimate erosional disequilibrium across drainage divides. We find that asymmetric emergence of Sumba Island created an initial parallel drainage, asymmetric across a divide that propagates landwards. Soon after establishing itself on the emerging slopes this drainage was disturbed by normal faulting, which has become the main force driving drainage rearrangement. Vertical offsets across normal fault scarps first triggered aggradation within valleys over the hanging walls, and then disconnected upstream reaches from downstream reaches, leading to the formation of wind gaps atop the fault scarps and upstream perched sedimentary basins. The defeat of rivers by growing fault scarps was catalysed by the possibility for surface water to be rerouted near the fault scarps into underground water networks inside the underlying carbonates. At the end of the process, the opposite drainage across the main water divide captured the struggling drainage. Capture mechanisms include initial groundwater capture of the perched alluvial aquifers, followed by ground sapping at the head of the opposite drainage and surface stream diversion by avulsion. Finally, normal faulting is the main driving force of drainage rearrangement allowing avulsion and karstic rerouting whereas asymmetric uplift and climate forcings have shown a low efficiency. The role of karstification is more ambiguous, catalysing or inhibiting drainage rearrangement. Copyright © 2018 John Wiley & Sons, Ltd.     

Simultaneous identification of parameter,initial condition,and boundary condition in groundwater modelling

In this paper, we perform an inverse method to simultaneously estimate aquifer parameters, initial condition, and boundary conditions in groundwater modelling. The parameter estimation is extended to a complete inverse problem that makes the calibrated groundwater flow model more realistic. The adjoint state method, the gradient search method, and the least square error algorithm are combined to build the optimization procedure. Horizontal two‐dimensional groundwater flow in a confined aquifer is exemplified to demonstrate the correlation between unknowns, the contribution of observation, as well as the suitability of applying the inverse method. The correlation analysis shows the connection between storage coefficient and initial condition. Besides, transmissivity and boundary conditions are also highly correlated. More observations at different location and time are necessary to provide sufficient information. A time series of unsteady head is requested for estimation of storage coefficient and initial condition. Observation near boundary is very effective for boundary condition estimation. The observation at pumping well mostly contributes to the estimation of transmissivity. According to all observations, it is possible to identify parameters, initial condition, and boundary condition simultaneously. Furthermore, the results not only illustrate the traditional assumption of known boundary condition but also initial condition, which may cause an incorrect estimation. Copyright © 2009 John Wiley & Sons, Ltd.     

Numerical simulation of groundwater flow patterns using flux as upper boundary

Since the 1960s, most of the studies on groundwater flow systems by analytical and numerical modelling have been based on given‐head upper boundaries. The disadvantage of the given‐head approach is that the recharge into and discharge from a basin vary with changes in hydraulic conductivity and/or basin geometry. Consequently, flow patterns simulated with given‐head boundaries but with different hydraulic conductivities and/or basin geometry may not reflect the effects of these variables. We conducted, therefore, numerical simulations of groundwater flow in theoretical drainage basins using flux as the upper boundary and realistically positioned fluid‐potential sinks while changing the infiltration intensity, hydraulic conductivities, and geometric configuration of the basin. The simulated results demonstrate that these variables are dominant factors controlling the flow pattern in a laterally closed drainage basin. The ratio of infiltration intensity to hydraulic conductivity (R_ic) has been shown to be an integrated pattern‐parameter in a basin with a given geometric configuration and possible fluid‐potential‐sink distribution. Successively, the changes in flow patterns induced by stepwise reductions in R_ic are identical, regardless of whether the reductions are due to a decrease in infiltration intensity or an increase in hydraulic conductivity. The calculated examples show five sequential flow patterns containing (i) only local, (ii) local–intermediate, (iii) local–intermediate–regional, (iv) local–regional, and (v) just regional flow systems. The R_ic was found to determine also whether a particular sink is active or not as a site of discharge. Flux upper boundary is preferable for numerical simulation when discussing the flow patterns affected by a change of infiltration, the hydraulic conductivity, or the geometry of a basin. Copyright © 2012 John Wiley & Sons, Ltd.     

Tracing contamination sources through phenotypic characterization of Escherichia coli isolates from surface water and groundwater in an agro-ecosystem

The objective of this research was to evaluate the groundwater chemical and bacteriological quality in the Barranquita-Knutzen basin (Córdoba, Argentina). The main purpose was to trace contamination through the examination of bacteriological parameters and antibiotic resistance of Escherichia coli, relating them to surface water, hydrogeological features and land use. Thus, 40 water samples were collected. The major chemical components and bacterial indicators were determined and antibiotic resistance was analysed using standard methods. Multivariate factorial analysis showed that the first principal component (PC) reveals the process of water mineralization, while the second and the third PCs explain a low percentage of variance, but collect chemical constituents and total and faecal coliform bacteria, respectively, revealing specific contamination situations. The observed antibiotic resistance profiles of E. coli and their relation with the land uses revealed that the source of faecal contamination in water is mainly from animal residues.     

Tidal effects on groundwater dynamics in unconfined aquifers

The variation of seawater level resulting from tidal fluctuations is usually neglected in regional groundwater flow studies. Although the tidal oscillation is damped near the shoreline, there is a quasi‐steady‐state rise in the mean water‐table position, which may have an influence on regional groundwater flow. In this paper the effects of tidal fluctuations on groundwater hydraulics are investigated using a variably saturated numerical model that includes the effects of a realistic mild beach slope, seepage face and the unsaturated zone. In particular the impact of these factors on the velocity field in the aquifer is assessed. Simulations show that the tidal fluctuation has substantial consequences for the local velocity field in the vicinity of the exit face, which affects the nearshore migration of contaminant in coastal aquifers. An overheight in the water table as a result of the tidal fluctuation is observed and this has a significant effect on groundwater discharge to the sea when the landward boundary condition is a constant water level. The effect of beach slope is very significant and simplifying the problem by considering a vertical beach face causes serious errors in predicting the water‐table position and the groundwater flux. For media with a high effective capillary fringe, the moisture retained above the water table is important in determining the effects of the tidal fluctuations. Copyright © 2001 John Wiley & Sons, Ltd.     

Heat as a groundwater tracer in shallow and deep heterogeneous media: Analytical solution,spreadsheet tool,and field applications

Groundwater flow advects heat, and thus, the deviation of subsurface temperatures from an expected conduction‐dominated regime can be analysed to estimate vertical water fluxes. A number of analytical approaches have been proposed for using heat as a groundwater tracer, and these have typically assumed a homogeneous medium. However, heterogeneous thermal properties are ubiquitous in subsurface environments, both at the scale of geologic strata and at finer scales in streambeds. Herein, we apply the analytical solution of Shan and Bodvarsson ( 2004 ), developed for estimating vertical water fluxes in layered systems, in 2 new environments distinct from previous vadose zone applications. The utility of the solution for studying groundwater‐surface water exchange is demonstrated using temperature data collected from an upwelling streambed with sediment layers, and a simple sensitivity analysis using these data indicates the solution is relatively robust. Also, a deeper temperature profile recorded in a borehole in South Australia is analysed to estimate deeper water fluxes. The analytical solution is able to match observed thermal gradients, including the change in slope at sediment interfaces. Results indicate that not accounting for layering can yield errors in the magnitude and even direction of the inferred Darcy fluxes. A simple automated spreadsheet tool (Flux‐LM) is presented to allow users to input temperature and layer data and solve the inverse problem to estimate groundwater flux rates from shallow (e.g., <1 m) or deep (e.g., up to 100 m) profiles. The solution is not transient, and thus, it should be cautiously applied where diel signals propagate or in deeper zones where multi‐decadal surface signals have disturbed subsurface thermal regimes.     

Evaluating the dual‐boundary forcing concept in subsurface–land surface interactions of the hydrological cycle

Subsurface and land surface processes (e.g. groundwater flow, evapotranspiration) of the hydrological cycle are connected via complex feedback mechanisms, which are difficult to analyze and quantify. In this study, the dual‐boundary forcing concept that reveals space–time coherence between groundwater dynamics and land surface processes is evaluated. The underlying hypothesis is that a simplified representation of groundwater dynamics may alter the variability of land surface processes, which may eventually affect the prognostic capability of a numerical model. A coupled subsurface–land surface model ParFlow.CLM is applied over the Rur catchment, Germany, and the mass and energy fluxes of the coupled water and energy cycles are simulated over three consecutive years considering three different lower boundary conditions (dynamic, constant, and free‐drainage) based on groundwater dynamics to substantiate the aforementioned hypothesis. Continuous wavelet transform technique is applied to analyze scale‐dependent variability of the simulated mass and energy fluxes. The results show clear differences in temporal variability of latent heat flux simulated by the model configurations with different lower boundary conditions at monthly to multi‐month time scales (~32–91 days) especially under soil moisture limited conditions. The results also suggest that temporal variability of latent heat flux is affected at even smaller time scales (~1–3 days) if a simple gravity drainage lower boundary condition is considered in the coupled model. This study demonstrates the importance of a physically consistent representation of groundwater dynamics in a numerical model, which may be important to consider in local weather prediction models and water resources assessments, e.g. drought prediction. Copyright © 2015 John Wiley & Sons, Ltd.     

On the importance of river hydrodynamics in simulating groundwater levels and baseflows

Research to date affirmed the key role of stream–aquifer interactions in integrated water resources management. The importance of river hydrodynamics on the spatial and temporal behaviour of groundwater was, however, not yet fully investigated. In contrast to the common approach where topography-based estimates of riverbed elevation may lead to inappropriate discretization and constant river stages, this study couples a fully hydrodynamic and one-dimensional river model to a two-dimensional catchment hydrological model. The surface and subsurface runoff, groundwater, and river components are integrated into a single modelling framework. The coupled model was applied to a medium sized catchment in Belgium with three model setups, in which the level of detail of representation of river hydrodynamics varies. Further model iterations were carried out for the most exhaustive setup to assess the importance of the bi-directional interactions between model components. Results show that higher details of river hydrodynamics help to improve the simulation of time-averaged groundwater levels. However, the impacts were not that clear for the time-varying groundwater levels. Moreover, visual and statistical model performance evaluation indicates a strong enhancement of the coupled models compared to the output from the hydrological model with respect to river discharge observations at catchment outlet and at internal stations. It also reveals the impact of river hydrodynamics on groundwater discharges when the most detailed setting delivered the highest performance among the three coupled models.     

Quantifying the role of karstic groundwater in a snowmelt-dominated hydrologic system

River discharge in mountainous regions of the world is often dominated by snowmelt, but base flows are sustained primarily by groundwater storage and discharge. Although numerous recent studies have focused on base-flow discharge in mountain systems, almost no work has explicitly investigated the role of karst groundwater in these systems across a full range of flow conditions. We directly measured groundwater discharge from 48 karst springs in the Kaweah River and its five forks in the Sierra Nevada mountains, California, United States. Relationships between spring and river discharge showed that karst aquifers and springs provide significant storage and delayed discharge to the river. Regression models showed that, of all potential seasonal groundwater storage compartments in the river basin, the area of karst (0.1–4.4%) present provides the best explanation of base-flow recession in each fork of the Kaweah River (directly measured contributions from karst springs ranged from 3.5 to 16% during high-flow to 20 to 65% during base-flow conditions). These results show that, even in settings where karst represents a small portion of basin area, it may play an over-sized role in seasonal storage and water resources in mountain systems. Karst aquifers are the single most important non-snow storage component in the Kaweah River basin, and likely provide similar water storage capacities and higher base flows in other mountain river systems with karst when compared with systems without karst.     

Surface water and groundwater interactions in an extensively mined watershed,upper Schuylkill River,Pennsylvania, USA

Streams crossing underground coal mines may lose flow, whereas abandoned mine drainage (AMD) restores flow downstream. During 2005–2012, discharge from the Pine Knot Mine Tunnel, the largest AMD source in the upper Schuylkill River Basin, had near‐neutral pH and elevated concentrations of iron, manganese and sulphate. Discharge from the tunnel responded rapidly to recharge but exhibited a prolonged recession compared with nearby streams, consistent with rapid infiltration of surface water and slow release of groundwater from the mine complex. Dissolved iron was attenuated downstream by oxidation and precipitation, whereas dissolved CO₂ degassed and pH increased. During high flow conditions, the AMD and downstream waters exhibited decreased pH, iron and sulphate with increased acidity that were modelled by mixing net‐alkaline AMD with recharge or run‐off having low ionic strength and low pH. Attenuation of dissolved iron within the river was least effective during high flow conditions because of decreased transport time coupled with inhibitory effects of low pH on oxidation kinetics. A numerical model of groundwater flow was calibrated by using groundwater levels in the Pine Knot Mine and discharge data for the Pine Knot Mine Tunnel and West Branch Schuylkill River during a snowmelt event in January 2012. Although the calibrated model indicated substantial recharge to the mine complex took place away from streams, simulation of rapid changes in mine pool level and tunnel discharge during a high flow event in May 2012 required a source of direct recharge to the Pine Knot Mine. Such recharge produced small changes in mine pool level and rapid changes in tunnel flow rate because of extensive unsaturated storage capacity and high transmissivity within the mine complex. Thus, elimination of stream leakage could have a small effect on the annual discharge from the tunnel, but a large effect on peak discharge and associated water quality downstream. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.     

Unexpected nationwide nitrate declines in groundwater of Korea

Elevated levels of nitrate in groundwater are an important concern for health and the environment. The overapplication of nitrogen fertilizer to croplands is one of the major sources of high nitrate content in groundwater. In this study, we analyse the nitrate concentrations in Korean groundwater based on data from groundwater quality monitoring wells (n = 1,022–2,072), which were sampled twice annually over a recent 13‐year analysis period (2001–2013). We report that groundwater nitrate levels are decreasing, despite steadily increasing groundwater use. The maximum nitrate concentration decreased from 168.91 to 48.11 mg/L, whereas the mean values also show a gradual decreasing trend. Non‐parametric Mann–Kendall tests on nitrate concentrations also confirm the decreasing trend. The nitrate decrease is more clearly evident in agricultural groundwater as compared to domestic and drinking groundwaters. This decrease of nitrate in groundwater coincides with a large decline in nitrogen fertilizer application due to reduced cropland areas, more sustainable agricultural practices, and progressive improvement of sewage disposal services. This study proposes that the long‐term adoption of best practices in agriculture has had a positive impact on groundwater nitrate control.     

Quantitative analysis of the driving factors for groundwater resource changes in arid irrigated areas

How to quantify the impact of climate change and human activities on groundwater is not only a hot topic of current research but also a key point of water resource management in arid irrigated areas. Therefore, this paper analyzes the changes in the trends of land use, climate, and groundwater extraction in the Yanqi Basin in recent years and uses the distributed hydrological model MIKE-SHE to quantitatively analyze the impacts of these three factors on groundwater resources. The results show that: 1. The Nash coefficients of the simulated and observed groundwater levels during the verification period are 0.84, 0.79 and 0.76; the correlation coefficient between the simulated and observed soil moisture is 0.86. Although there are some uncertainties in the simulation, the results prove that the model can be used to simulate arid irrigated areas. 2. The effects of these three factors on groundwater levels are 5, 12.5 and 82.5%, respectively, and have caused the regional average groundwater level to decrease by a maximum of 0.07, 0.23 and 1.79 m, respectively. The effects of these three factors on the interactions between surface water and groundwater were 7.04, 3.63 and 89.33%. Groundwater extraction has become the main influencing factor of regional groundwater resources changes due to its more direct influence. 3. The influence of groundwater extraction has a strong spatial distribution characteristic and 10% of the study area has been greatly impacted by the groundwater extraction. Base on the above results, integrating multidisciplinary knowledge to establish the relationship between ecological environment and groundwater changes can provide strategies for the sustainable development of groundwater.     

Conceptual and numerical models for groundwater flow in an arid inland river basin

The Heihe River Basin (HRB) is an inland watershed in northwest China with a total area of approximately 130,000 km², stretching from the Qilian Mountains in the south to the oases and agricultural fields in the middle and further to the Gobi desert in the north bordering Mongolia. As part of a major ecohydrological research initiative to provide a stronger scientific underpinning for sustainable water management in arid ecosystems, a regional‐scale integrated ecological and hydrological model is being developed, incorporating the knowledge based on the results of environmental isotope tracer analysis and the multiscale observation datasets. The first step in the model development effort is to construct and calibrate a groundwater flow model for the middle and lower HRB where the oases and vegetation along the Heihe river corridor are highly dependent on groundwater. In this study, the software tool ‘Arc Hydro Groundwater’ is used to build and visualize a hydrogeological data model for the HRB that links all relevant spatiotemporal hydrogeological data in a unified geodatabase within the ArcGIS environment. From the conceptual model, a regional‐scale groundwater flow model has been developed using MODFLOW‐2005. Critical considerations in developing the flow model include the representation of mountainous terrains and fluvial valleys by individual model layers, treatment of aquifer heterogeneities across multiple scales and selection of proper observation data and boundary conditions for model calibration. This paper discusses these issues in the context of the Heihe River Basin, but the results and insights from this study will have important implications for other large, regional groundwater modelling studies, especially in arid and semiarid inland river basins. Copyright © 2014 John Wiley & Sons, Ltd.