Directions of preferential flow in a hillslope soil, 1. Quasi‐steady flow

Preferred infiltration is mainly perceived as vertically down whereas subsurface storm flow is thought to occur parallel to slopes. The transition from vertical to lateral flow in a layered hillslope soil is the focus of the contribution. Transient flow is assumed to move as a wetting front. Three time‐domain reflectometry (TDR) wave‐guides, each 0·15 m long, were mounted in the shape of a truncated tetrahedron with its peak pointing down. Each wave‐guide focuses the front velocity along its axis. The three front‐velocity vectors are decomposed into their x, y and z components, which are then assembled to the resultant velocity vector. The volume density flux of preferred flow is the product of the front velocity and the mobile water content. The latter is the amplitude of transient soil moisture measured with each wave‐guide. The resultant vector of the volume flux density is computed similarly to the velocity vector. The experimental approach allows for the rapid assessment of transient flows without relying on the variation of water potentials. The experiments indicate that the directions of the resultant vectors of velocity and volume flux density can be estimated if the moisture variations of the three TDR wave‐guides are strongly correlated during the passing of the wetting front. Copyright © 2004 John Wiley & Sons, Ltd.     

Characteristics of preferential flow and groundwater discharge to Shingobee Lake,Minnesota, USA

Small‐scale heterogeneities and large changes in hydraulic gradient over short distances can create preferential groundwater flow paths that discharge to lakes. A 170 m² grid within an area of springs and seeps along the shore of Shingobee Lake, Minnesota, was intensively instrumented to characterize groundwater‐lake interaction within underlying organic‐rich soil and sandy glacial sediments. Seepage meters in the lake and piezometer nests, installed at depths of 0·5 and 1·0 m below the ground surface and lakebed, were used to estimate groundwater flow. Statistical analysis of hydraulic conductivity estimated from slug tests indicated a range from 21 to 4·8 × 10^?3 m day^?1 and small spatial correlation. Although hydraulic gradients are overall upward and toward the lake, surface water that flows onto an area about 2 m onshore results in downward flow and localized recharge. Most flow occurred within 3 m of the shore through more permeable pathways. Seepage meter and Darcy law estimates of groundwater discharge agreed well within error limits. In the small area examined, discharge decreases irregularly with distance into the lake, indicating that sediment heterogeneity plays an important role in the distribution of groundwater discharge. Temperature gradients showed some relationship to discharge, but neither temperature profiles nor specific electrical conductance could provide a more convenient method to map groundwater–lake interaction. These results suggest that site‐specific data may be needed to evaluate local water budget and to protect the water quality and quantity of discharge‐dominated lakes. Copyright © 2002 John Wiley & Sons, Ltd.     

Mixing of event and pre‐event water in a shallow Entisol in sloping farmland based on isotopic and hydrometric measurements,SW China

Water percolation and flow processes in subsurface geologic media play an important role in determining the water source for plants and the transport of contaminants or nutrients, which is essential for water resource management and the development of measures for pollution mitigation. During June 2013, the dynamics of the rainwater, soil water, subsurface flows and groundwater in a shallow Entisol on sloping farmland were monitored using a hydrometric and isotopic approach. The results showed that effective mixing of rainwater and soil water occurred in hours. The rebound phenomenon of δD profiles in soils showed that most isotope‐depleted rainwater largely bypassed the soil matrix when the water saturation in the soil was high. Preferential‐flow, which was the dominant water movement pattern in the vadose zone, occurred through the whole soil profile, and infrequent piston‐flow was mainly found at 20–40 cm in depth. The interflow in the soil layer, composed of 75.2% rainwater, was only generated when the soil profile had been saturated. Underflow in the fractured mudrock was the dominant flow type in this hillslope, and outflow was dominated by base flow (groundwater flow) with a mean contribution of 76.7%. The generation mechanism of underflow was groundwater ridging, which was superimposed upon preferential‐flow composed mainly of rainwater. The quick mixing process of rainwater and soil water and the rapid movement of the mixture through preferential channels in the study soil, which shows a typical bimodal pore size distribution, can explain the prompt release of pre‐event water in subsurface flow. Water sources of subsurface flows at peak discharge could be affected by the antecedent soil water content, rain characteristics and antecedent groundwater levels. Copyright © 2016 John Wiley & Sons, Ltd.     

Macropores and preferential flow—a love‐hate relationship

Preferential flow is of high relevance for runoff generation, transport of chemicals and nutrients, and the transit time distribution of water in the soil or watershed. However, preferential flow effects are generally ignored in lumped hydrological models. And even most physically‐based models ignore macropores and preferential flow features at the soil and hillslope scale. Keith Beven was never satisfied with this situation and he tried again and again to convince the scientific community to focus their research on the complex topic of macropore and preferential flow. Although he recognized how difficult it is to correctly include preferential flow in hydrological models, he made substantial progress defining and describing macropore flow and showing its relevance, developing models to simulate preferential flow, and in particular, the interaction between macropores and the soil matrix. In this short commentary, I reflect on these achievements and outline a vision for research in preferential flow experiments and modeling.     

Catchment‐scale conceptual modelling of water and solute transport in the dual flow system of the karst critical zone

Hydrological and hydrochemical processes in the critical zone of karst environments are controlled by the fracture‐conduit network. Modelling hydrological and hydrochemical dynamics in such heterogeneous hydrogeological settings remains a research challenge. In this study, water and solute transport in the dual flow system of the karst critical zone were investigated in a 73.5‐km² catchment in southwest China. We developed a dual reservoir conceptual run‐off model combined with an autoregressive and moving average model with algorithms to assess dissolution rates in the “fast flow” and “slow flow” systems. This model was applied to 3 catchments with typical karst critical zone architectures, to show how flow exchange between fracture and conduit networks changes in relation to catchment storage dynamics. The flux of bidirectional water and solute exchange between the fissure and conduit system increases from the headwaters to the outfall due to the large area of the developed conduits and low hydraulic gradient in the lower catchment. Rainfall amounts have a significant influence on partitioning the relative proportions of flow and solutes derived from different sources reaching the underground outlet. The effect of rainfall on catchment function is modulated by the structure of the karst critical zone (e.g., epikarst and sinkholes). Thin epikarst and well‐developed sinkholes in the headwaters divert more surface water (younger water) into the underground channel network, leading to a higher fraction of rainfall recharge into the fast flow system and total outflow. Also, the contribution of carbonate weathering to mass export is also higher in the headwaters due to the infiltration of younger water with low solute concentrations through sinkholes.     

A heat pulse technique for the determination of small‐scale flow directions and flow velocities in the streambed of sand‐bed streams

The hyporheic zone (HZ) has the capability to eliminate and attenuate nutrients and contaminants in riverine systems. Biogeochemical reactions and the potential elimination of contaminants are strongly controlled by the flow paths and dynamics in the HZ. Nevertheless, an easily applicable method for the field determination of flow patterns in the HZ is still lacking. Therefore, a heat pulse technique, which traces the movement of a short heat pulse in the upper part of the HZ and other sand beds, was developed. Five rods are vertically driven into the sediment of the streambed; one rod with a heater as point source located in about 10‐cm sediment depth and four rods with four temperature sensors in 3 cm distance, arranged concentrically with 7 cm diameter around the heating rod. Subsequently, a heat pulse is applied and the resulting breakthrough curves are indicative of flow velocities and flow directions in the streambed. A rough data analysis procedure is also suggested. In addition, laboratory experiments were performed to test the heat pulse technique. These experiments were validated based on coupled numerical modelling of flow and heat transport. First field tests of the method prove that the method is easily applicable under field conditions. These first field tests showed highly complex flow patterns with flow velocities from 1·8 to 4·9 cm min^?1 and flow directions from parallel to surface flow to opposite to surface flow. This suggests the need for a robust method to quantify hyporheic flow patterns in situ. Copyright © 2011 John Wiley & Sons, Ltd.     

Modelling two‐dimensional steady‐state groundwater flow and flow sensitivity to boundary conditions in blanket peat complexes

This study used a two‐dimensional steady‐state finite‐element groundwater flow model to simulate groundwater flow in two Newfoundland blanket peat complexes and to examine flow system sensitivity to changes in water table recharge and aquifer properties. The modelling results were examined within the context of peat‐forming processes in the two complexes. Modelled flow compared favourably with observed flow. The sensitivity analyses suggested that more highly decomposed bog peat along bog margins probably has/had a positive impact on net peat accumulation within bog interiors. Peat with lower hydraulic conductivity along bog margins effectively impedes lateral drainage, localizes water table drawdown to extreme bog margins, and elevates water tables along bog interiors. Peat formation and elevated water tables in adjacent poor fens/laggs currently rely on placic and ortstein horizons impeding vertical drainage and water flow inputs from adjacent bogs. Modest reductions in atmospheric recharge were found to govern bog‐flow‐system geometries in a way that would adversely affect paludification processes in adjacent fens/laggs. Copyright © 2004 John Wiley & Sons, Ltd.     

The influence of preferential flow on hillslope hydrology in a semi‐arid watershed (in the Spanish Dehesas)

Preferential flow is known to influence hillslope hydrology in many areas around the world. Most research on preferential flow has been performed in temperate regions. Preferential infiltration has also been found in semi‐arid regions, but its impact on the hydrology of these regions is poorly known. The aim of this study is to describe and quantify the influence of preferential flow on the hillslope hydrology from small scale (infiltration) to large scale (subsurface stormflow) in a semi‐arid Dehesa landscape. Precipitation, soil moisture content, piezometric water level and discharge data were used to analyse the hydrological functioning of a catchment in Spain. Variability of soil moisture content during the transition from dry to wet season (September to November) within horizontal soil layers leads to the conclusion that there is preferential infiltration into the soils. When the rainfall intensity is high, a water level rapidly builds up in the piezometer pipes in the area, sometimes even reaching soil surface. This water level also drops back to bedrock within a few hours (under dry catchment conditions) to days (under wet catchment conditions). As the soil matrix is not necessarily wet while this water layer is built up, it is thought to be a transient water table in large connected pores which drain partly to the matrix, partly fill up bedrock irregularities and partly drain through subsurface flow to the channels. When the soil matrix becomes wetter the loss of water from macropores to the matrix and bedrock decreases and subsurface stormflow increases. It may be concluded that the hillslope hydrological system consists of a fine matrix domain and a macropore domain, which have their own flow characteristics but which also interact, depending on the soil matrix and macropore moisture contents. The macropore flow can result in subsurface flow, ranging from 13% contribution to total discharge for a large event of high intensity rainfall or high discharge to 80% of total discharge for a small event with low intensity rainfall or low discharge. During large events the fraction of subsurface stormflow in the discharge is suppressed by the large amount of surface runoff. Copyright © 2008 John Wiley & Sons, Ltd.     

Gypsies in the palace: experimentalist's view on the use of 3‐D physics‐based simulation of hillslope hydrological response

As a fundamental unit of the landscape, hillslopes are studied for their retention and release of water and nutrients across a wide range of ecosystems. The understanding of these near‐surface processes is relevant to issues of runoff generation, groundwater–surface water interactions, catchment export of nutrients, dissolved organic carbon, contaminants (e.g. mercury) and ultimately surface water health. We develop a 3‐D physics‐based representation of the Panola Mountain Research Watershed experimental hillslope using the TOUGH2 sub‐surface flow and transport simulator. A recent investigation of sub‐surface flow within this experimental hillslope has generated important knowledge of threshold rainfall‐runoff response and its relation to patterns of transient water table development. This work has identified components of the 3‐D sub‐surface, such as bedrock topography, that contribute to changing connectivity in saturated zones and the generation of sub‐surface stormflow. Here, we test the ability of a 3‐D hillslope model (both calibrated and uncalibrated) to simulate forested hillslope rainfall‐runoff response and internal transient sub‐surface stormflow dynamics. We also provide a transparent illustration of physics‐based model development, issues of parameterization, examples of model rejection and usefulness of data types (e.g. runoff, mean soil moisture and transient water table depth) to the model enterprise. Our simulations show the inability of an uncalibrated model based on laboratory and field characterization of soil properties and topography to successfully simulate the integrated hydrological response or the distributed water table within the soil profile. Although not an uncommon result, the failure of the field‐based characterized model to represent system behaviour is an important challenge that continues to vex scientists at many scales. We focus our attention particularly on examining the influence of bedrock permeability, soil anisotropy and drainable porosity on the development of patterns of transient groundwater and sub‐surface flow. Internal dynamics of transient water table development prove to be essential in determining appropriate model parameterization. Copyright © 2010 John Wiley & Sons, Ltd.     

Reconstruction of multi‐decadal groundwater level time‐series using a lumped conceptual model

Multi‐decadal groundwater level records, which provide information about long‐term variability and trends, are relatively rare. Whilst a number of studies have sought to reconstruct river flow records, there have been few attempts to reconstruct groundwater level time‐series over a number of decades. Using long rainfall and temperature records, we developed and applied a methodology to do this using a lumped conceptual model. We applied the model to six sites in the UK, in four different aquifers: Chalk, limestone, sandstone and Greensand. Acceptable models of observed monthly groundwater levels were generated at four of the sites, with maximum Nash–Sutcliffe Efficiency scores of between 0.84 and 0.93 over the calibration and evaluation periods, respectively. These four models were then used to reconstruct the monthly groundwater level time‐series over approximately 60 years back to 1910. Uncertainty in the simulated levels associated with model parameters was assessed using the Generalized Likelihood Uncertainty Estimation method. Known historical droughts and wet period in the UK are clearly identifiable in the reconstructed levels, which were compared using the Standardized Groundwater Level Index. Such reconstructed records provide additional information with which to improve estimates of the frequency, severity and duration of groundwater level extremes and their spatial coherence, which for example is important for the assessment of the yield of boreholes during drought periods. Copyright © 2016 British Geological Survey. Hydrological Processes © 2016 John Wiley & Sons Ltd     

A low‐dimensional hillslope‐based catchment model for layered groundwater flow

Despite the strong interaction between surface and subsurface waters, groundwater flow representation is often oversimplified in hydrological models. For instance, the interplay between local or shallow aquifers and deeper regional‐scale aquifers is typically neglected. In this work, a novel hillslope‐based catchment model for the simulation of combined shallow and deep groundwater flow is presented. The model consists of the hillslope‐storage Boussinesq (hsB) model representing shallow groundwater flow and an analytic element (AE) model representing deep regional groundwater flow. The component models are iteratively coupled via a leakage term based on Darcy's law, representing delayed recharge to the regional aquifer through a low conductivity layer. Simulations on synthetic single hillslopes and on a two‐hillslope open‐book catchment are presented, and the results are compared against a benchmark three‐dimensional Richards equation model. The impact of hydraulic conductivity, hillslope plan geometry (uniform, convergent, divergent), and hillslope inclination (0.2%, 5%, and 30%) under drainage and recharge conditions are examined. On the single hillslopes, good matches for heads, hydrographs, and exchange fluxes are generally obtained, with the most significant differences in outflows and heads observed for the 30% slope and for hillslopes with convergent geometry. On the open‐book catchment, cumulative outflows are overestimated by 1–4%. Heads in the confined and unconfined aquifers are adequately reproduced throughout the catchment, whereas exchange fluxes are found to be very sensitive to the hillslope drainable porosity. The new model is highly efficient computationally compared to the benchmark model. The coupled hsB/AE model represents an alternative to commonly used groundwater flow representations in hydrological models, of particular appeal when surface–subsurface exchanges, local aquifer–regional aquifer interactions, and low flows play a key role in a watershed's dynamics. Copyright © 2011 John Wiley & Sons, Ltd.     

The relevance of preferential flow in catchment scale simulations: Calibrating a 3D dual-permeability model using DREAM

The occurrence of preferential flow in the subsurface has often been shown in field experiments. However, preferential flow is rarely included in models simulating the hydrological response at the catchment scale. If it is considered, preferential flow parameters are typically determined at the plot scale and then transferred to larger-scale simulations. Here, we successfully used the optimization algorithm DiffeRential Evolution Adaptive Metropolis (DREAM) to calibrate a 3D physics-based dual-permeability model directly at the catchment scale. In order to keep computational costs of the optimization routine at a reasonable level, we limited the number of parameters to be calibrated to the ones that had been shown before to be most influential for the simulation of discharge. We also calibrated parameters of the matrix domain and the macropore domain with a fixed parameter ratio between soil layers instead of calibrating every layer separately. These ratios reflected observed depth profiles of soil hydraulic properties at our study site. The dual-permeability parameter sets identified during calibration were able to simulate observed discharge time series satisfactorily but did not outperform a calibrated single-domain reference model scenario. Saturated hydraulic conductivities of the macropore domain were calibrated such that they became very similar to matrix saturated hydraulic conductivities, thereby effectively removing the effect of macropores. This suggests that the incorporation of vertical preferential flow as represented by the dual-permeability approach was not relevant for reproducing the hydrometric response reasonably well in the studied catchment. We also tested the scale-invariance of the calibrated dual-permeability parameter sets by using the parameter sets performing best at catchment scale to simulate plot-scale bromide depth profiles obtained from tracer irrigation experiments. This parameter transfer proved to be not successful, indicating that soil hydraulic parameters are scale-variant, independent of the direction of parameter transfer.     

Fine‐scale characteristics of groundwater flow in a peatland

Fine‐scale dynamics of groundwater flow were studied in a 1·5 ha peatland in central New York. Measurements of the hydraulic head throughout a detailed network of piezometer clusters revealed spatial and temporal variability in the direction of groundwater flow at a very fine (within a few metres) scale of analysis. Within the small wetland, there were areas of groundwater recharge, discharge and lateral flow. Such patterns of groundwater flow frequently reversed or changed due to fluctuations of only a few centimetres in hydraulic head. Specific conductance, deuterium signatures and calcium concentrations of groundwater corroborated the groundwater flow patterns determined with hydraulic head measurements and illustrated the influence of source water chemistry and evaporation on different layers in the peat column. The control of peat chemistry by such fine‐scale groundwater flow may have important implications for plant community composition and diversity in groundwater‐fed peatlands. Copyright © 1999 John Wiley & Sons, Ltd.     

A simulation of large‐scale groundwater flow and travel time in a fractured rock environment for waste disposal purposes

Two‐dimensional regional groundwater flow was simulated based on a conceptual model of low‐permeability crystalline rocks of the Whiteshell Research Area (WRA) in south‐eastern Manitoba. The conceptual model consists of fracture zones that strike in different directions and dip at various angles in the background rock mass. The thickness and hydraulic properties of the fracture zones in the conceptual model were varied as were the fluid properties and the boundary conditions of the groundwater flow system. The effects of these variations on the groundwater flow pattern and on the convective travel time along pathways from a hypothetical disposal vault at 500 m depth to discharge locations at the ground surface were evaluated. The vault was located in the regional discharge area of the groundwater system. A homogeneous conceptual model of the WRA, having only freshwater flow, formed a groundwater flow pattern with a regional flow system. Local flow systems developed increasingly with the introduction of fracture zones 20 m and 3 m thick, and depth‐dependent fluid density. This indicates a reduction in groundwater residence time by fracture zones and fluid density. Flow pathways were analysed using both a stream‐function and a particle‐tracking technique. The pathways and their lengths from the location of the vault to the surface varied spatially according to the flow patterns. The minimum travel time along these pathways was less than 150 000 and greater than 4 000 000 years in models with and without fracture zones, respectively, indicating that the presence of fracture zones was the major controlling factor. A precise knowledge and refinement of conceptual model parameters is necessary during site selection for waste disposal purposes. Copyright © 2004 John Wiley & Sons, Ltd.     

Understanding soil‐pipe flow and its role in ephemeral gully erosion

The role of soil pipeflow in ephemeral gully erosion is not well understood. Experiments were conducted on continuous soil pipes to better understand the role of internal erosion of soil pipes and its relation to ephemeral gully development. Soil beds of 140 cm length, 100 cm width and 20 cm depth had a single soil pipe of different initial sizes (2, 4, 6, 8, and 10 mm diameter) extend from a water reservoir to the outlet. Experiments were run on Providence silt loam and Smithdale loam soils under a constant head of 15 cm established for 30 min. Either the tunnel collapsed or the head could not be maintained. Soil pipes that were initially 2 and 4 mm clogged instantaneously at their mouth and did not exhibit flow, whereas, pipes initially ≥ 6 mm enlarged by 268, 397, and 699% on average for the 6, 8, and 10 mm diameters, respectively. Critical shear stress values were found to be essentially zero, and erodibility values gave erosion indexes that were extremely high. The rapid internal erosion resulted in erratic flow and sediment concentrations with periods of no flow as pipes were temporarily clogged followed by surges of high flow and high sediment concentrations. Tensiometers within 6 cm of the soil pipes did not exhibit pressure increases typically associated with pipe clogging. Flow through 10 mm diameter soil pipes exhibited tunnel collapse for both soils tested. Tunnel collapse typically occurred within minutes of flow establishment suggesting that ephemeral gullies could be misinterpreted as being caused by convergent surface flow if observations were made after the runoff event instead of when flow is first established through soil pipes. Copyright © 2011 John Wiley & Sons, Ltd.     

Stormflow generation involving pipe flow in a zero‐order basin of Peninsular Malaysia

Hydrological responses in a zero‐order basin (ZOB), a portion of whose discharge emerged via preferential flow through soil pipes, were examined over a 2‐year period in Peninsular Malaysia to elucidate primary stormflow generation processes. Silicon (Si) and specific conductance (EC) in various runoff components were also measured to identify their sources. ZOB flow response was dependent on antecedent precipitation amount; runoff increased linearly with precipitation during events >20 mm in relatively wet antecedent moisture conditions. Runoff derived from direct precipitation falling onto saturated areas accounted for <0·2% of total ZOB flow volume during the study period, indicating the predominance of subsurface pathways in ZOB flow. ZOB flow (high EC and low Si) was distinct from perennial baseflow via bedrock seepage (low EC and high Si) 5 m downstream of the ZOB outlet. Pipe flow responded quickly to ZOB flow rate and was characterized by a threshold flow capacity unique to each pipe. Piezometric data and pipe flow records demonstrated that pipes located deeper in the soil initiated first, followed by those at shallower depths; initiation of pipe flow corresponded to shallow groundwater rise above the saprolite‐soil interface. Chemical signatures of pipe flow were similar to each other and to the ZOB flow, suggesting that the sources were well‐mixed soil‐derived shallow groundwater. Based upon the volume of pipe flow during storms, the combined contribution of the pipes monitored accounted for 48% of total ZOB flow during the study period. Our results suggest that shallow groundwater, possibly facilitated by preferential flow accreted above the saprolite–soil interface, provides dominant stormflow, and that soil pipes play an important role in the rapid delivery of solute‐rich water to the stream system. Copyright © 2006 John Wiley & Sons, Ltd.     

Effect of variable‐density groundwater flow on nitrate flux to coastal waters

A two‐dimensional variable‐density groundwater flow and transport model was developed to provide a conceptual understanding of past and future conditions of nitrate (NO₃) transport and estimate groundwater nitrate flux to the Gulf of Mexico. Simulation results show that contaminant discharge to the coast decreases as the extent of saltwater intrusion increases. Other natural and/or artificial surface waters such as navigation channels may serve as major sinks for contaminant loading and act to alter expected transport pathways discharging contaminants to other areas. Concentrations of NO₃ in the saturated zone were estimated to range between 30 and 160 mg?L^?1 as NO₃. Relatively high hydraulic vertical gradients and mixing likely play a significant role in the transport processes, enhancing dilution and contaminant migration to depth. Residence times of NO₃ in the deeper aquifers vary from 100 (locally) to about 300 years through the investigated aquifer system. NO₃ mass fluxes from the shallow aquifers (0 to 5.7 × 10⁴ mg?m^?2?day^?1) were primarily directed towards the navigation channel, which intersects and captures a portion of the shallow groundwater flow/discharge. Direct NO₃ discharge to the sea (i.e. Gulf of Mexico) from the shallow aquifer was very low (0 to 9.0 × 10¹ mg · m^?2?day^?1) compared with discharge from the deeper aquifer system (0 to 8.2 × 10³ mg?m^?2?day^?1). Both model‐calibrated and radiocarbon tracer‐determined contaminant flux estimates reveal similar discharge trends, validating the use of the model for density‐dependent flow conditions. The modelling approach shows promise to evaluate contaminant and nutrient loading for similar coastal regions worldwide. Copyright © 2015 John Wiley & Sons, Ltd.     

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.