Comparing MODFLOW simulation options for predicting intra‐meander flux

During the evolution of meander bends, the intra‐meander groundwater head gradients steepen and generate zones of accelerated water and nutrient intra‐meander fluxes important for ecosystem processes. This paper compares and contrasts three MODFLOW groundwater model packages based on their simulation of intra‐meander flux for two stages of meander evolution observed in a sandbox river table and one level of river bed clogging, where the hydraulic conductivity in the river bed is lower than in the adjacent aquifer. These packages are the Time‐Variant Specified Head package [constant head (CHD)], River package (RIV), and Streamflow‐Routing package (SFR2), each controlling the groundwater or river head bounding the intra‐meander region. The RIV and SFR2 packages fix river stage and allow for variation in groundwater head below the river, which is suggested for simulating intra‐meander flux for all sinuosities with and without river bed clogging whenever river bed parameters are available. The CHD package fixes below river groundwater head and fails to simulate intra‐meander head loss and flux in meanders with high sinuosity or river bed clogging. In low sinuosity meanders and in cases without river bed clogging, there were no significant differences between MODFLOW packages for simulating river intra‐meander head loss and flux. This research demonstrates why MODFLOW users need to consider the limitations of each package when simulating intra‐meander flux in reaches with river bed clogging, high sinuosity, or similarly steep hydraulic gradients. Copyright © 2014 John Wiley & Sons, Ltd.     

Application of an integrated surface water‐groundwater model to multi‐aquifers modeling in Choushui River alluvial fan,Taiwan

This research proposes a combination of SWAT and MODFLOW, MD‐SWAT‐MODFLOW, to address the multi‐aquifers condition in Choushui River alluvial fan, Taiwan. The natural recharge and unidentified pumping/recharge are separately estimated. The model identifies the monthly pumping/recharge rates in multi‐aquifers so that the daily streamflow can be simulated correctly. A multi‐aquifers condition means a subsurface formation composed of at least the unconfined aquifer, the confined aquifer, and an in‐between aquitard. In such a case, the variation of groundwater level is related to pumping/recharge activities in vertically adjacent aquifer and the river‐aquifer interaction. Both factors in turn affect the streamflow performance. Results show that MD‐SWAT‐MODFLOW performs better than SWAT alone in terms of simulated streamflow, especially during low flow period, when pumping/recharge rates are properly estimated. A sensitivity analysis of individual parameter suggests that the vertical leakance may be the most sensitive among all investigated MODFLOW parameters in terms of the estimated pumping/recharge among aquifers, and the Latin‐Hypercube‐One‐factor‐At‐a‐Time sensitivity analysis indicates that the hydraulic conductivity of channel is the most sensitive to the model performance. It also points out the necessity to simultaneously estimate pumping/recharge rates in multi‐aquifers. The estimated net pumping rate can be treated as a lower bound of the actual local pumping rate. As a whole, the model provides the spatio‐temporal groundwater use, which gives the authorities insights to manage groundwater resources. Copyright © 2012 John Wiley & Sons, Ltd.     

A conceptual–numerical model to simulate hydraulic head in aquifers that are hydraulically connected to surface water bodies

In this paper, we present a conceptual‐numerical model that can be deduced from a calibrated finite difference groundwater‐flow model, which provides a parsimonious approach to simulate and analyze hydraulic heads and surface water body–aquifer interaction for linear aquifers (linear response of head to stresses). The solution of linear groundwater‐flow problems using eigenvalue techniques can be formulated with a simple explicit state equation whose structure shows that the surface water body–aquifer interaction phenomenon can be approached as the drainage of a number of independent linear reservoirs. The hydraulic head field could be also approached by the summation of the head fields, estimated for those reservoirs, defined over the same domain set by the aquifer limits, where the hydraulic head field in each reservoir is proportional to a specific surface (an eigenfunction of an eigenproblem, or an eigenvector in discrete cases). All the parameters and initial conditions of each linear reservoir can be mathematically defined in a univocal way from the calibrated finite difference model, preserving its characteristics (geometry, boundary conditions, hydrodynamic parameters (heterogeneity), and spatial distribution of the stresses). We also demonstrated that, in practical cases, an accurate solution can be obtained with a reduced number of linear reservoirs. The reduced computational cost of these solutions can help to integrate the groundwater component within conjunctive use management models. Conceptual approximation also facilitates understanding of the physical phenomenon and analysis of the factors that influence it. A simple synthetic aquifer has been employed to show how the conceptual model can be built for different spatial discretizations, the parameters required, and their influence on the simulation of hydraulic head fields and stream–aquifer flow exchange variables. A real‐world case was also solved to test the accuracy of the proposed approaches, by comparing its solution with that obtained using finite‐difference MODFLOW code. Copyright © 2011 John Wiley & Sons, Ltd.     

Implementation of Solute Transport in the Vadose Zone into the “HYDRUS Package for MODFLOW”

The “HYDRUS package for MODFLOW” is an existing MODFLOW package that allows MODFLOW to simultaneously evaluate transient water flow in both unsaturated and saturated zones. The package is based on incorporating parts of the HYDRUS-1D model (to simulate unsaturated water flow in the vadose zone) into MODFLOW (to simulate saturated groundwater flow). The coupled model is effective in addressing spatially variable saturated-unsaturated hydrological processes at the regional scale. However, one of the major limitations of this coupled model is that it does not have the capability to simulate solute transport along with water flow and therefore, the model cannot be employed for evaluating groundwater contamination. In this work, a modified unsaturated flow and transport package (modified HYDRUS package for MODFLOW and MT3DMS) has been developed and linked to the three-dimensional (3D) groundwater flow model MODFLOW and the 3D groundwater solute transport model MT3DMS. The new package can simulate, in addition to water flow in the vadose zone, also solute transport involving many biogeochemical processes and reactions, including first-order degradation, volatilization, linear or nonlinear sorption, one-site kinetic sorption, two-site sorption, and two-kinetic sites sorption. Due to complex interactions at the groundwater table, certain modifications of the pressure head (compared to the original coupling) and solute concentration profiles were incorporated into the modified HYDRUS package. The performance of the newly developed model is evaluated using HYDRUS (2D/3D), and the results indicate that the new model is effective in simulating the movement of water and contaminants in the saturated-unsaturated flow domains.     

Reducing monitoring gaps at the aquifer–river interface by modelling groundwater–surface water exchange flow patterns

This study investigates spatial patterns and temporal dynamics of aquifer–river exchange flow at a reach of the River Leith, UK. Observations of sub‐channel vertical hydraulic gradients at the field site indicate the dominance of groundwater up‐welling into the river and the absence of groundwater recharge from surface water. However, observed hydraulic heads do not provide information on potential surface water infiltration into the top 0–15 cm of the streambed as these depths are not covered by the existing experimental infrastructure. In order to evaluate whether surface water infiltration is likely to occur outside the ‘window of detection’, i.e. the shallow streambed, a numerical groundwater model is used to simulate hydrological exchanges between the aquifer and the river. Transient simulations of the successfully validated model (Nash and Sutcliff efficiency of 0·91) suggest that surface water infiltration is marginal and that the possibility of significant volumes of surface water infiltrating into non‐monitored shallow streambed sediments can be excluded for the simulation period. Furthermore, the simulation results show that with increasing head differences between river and aquifer towards the end of the simulation period, the impact of streambed topography and hydraulic conductivity on spatial patterns of exchange flow rates decreases. A set of peak flow scenarios with altered groundwater‐surface water head gradients is simulated in order to quantify the potential for surface water infiltration during characteristic winter flow conditions following the observation period. The results indicate that, particularly at the beginning of peak flow conditions, head gradients are likely to cause substantial increase in surface water infiltration into the streambed. The study highlights the potential for the improvement of process understanding of hyporheic exchange flow patterns at the stream reach scale by simulating aquifer‐river exchange fluxes with a standard numerical groundwater model and a simple but robust model structure and parameterization. Copyright © 2011 John Wiley & Sons, Ltd.     

A New Package in MODFLOW to Simulate Unconfined Groundwater Flow in Sloping Aquifers

The nonhorizontal‐model‐layer (NHML) grid system is more accurate than the horizontal‐model‐layer grid system to describe groundwater flow in an unconfined sloping aquifer on the basis of MODFLOW‐2000. However, the finite‐difference scheme of NHML was based on the Dupuit‐Forchheimer assumption that the streamlines were horizontal, which was acceptable for slope less than 0.10. In this study, we presented a new finite‐difference scheme of NHML based on the Boussinesq assumption and developed a new package SLOPE which was incorporated into MODFLOW‐2000 to become the MODFLOW‐SP model. The accuracy of MODFLOW‐SP was tested against solution of Mac Cormack (1969). The differences between the solutions of MODFLOW‐2000 and MODFLOW‐SP were nearly negligible when the slope was less than 0.27, and they were noticeable during the transient flow stage and vanished in steady state when the slope increased above 0.27. We established a model considering the vertical flow using COMSOL Multiphysics to test the robustness of constrains used in MODFLOW‐SP. The results showed that streamlines quickly became parallel with the aquifer base except in the narrow regions near the boundaries when the initial flow was not parallel to the aquifer base. MODFLOW‐SP can be used to predict the hydraulic head of an unconfined aquifer along the profile perpendicular to the aquifer base when the slope was smaller than 0.50. The errors associated with constrains used in MODFLOW‐SP were small but noticeable when the slope increased to 0.75, and became significant for the slope of 1.0.     

Studying the Flow Dynamics of a Karst Aquifer System with an Equivalent Porous Medium Model

The modeling of groundwater flow in karst aquifers is a challenge due to the extreme heterogeneity of its hydraulic parameters and the duality in their discharge behavior, that is, rapid response of highly conductive karst conduits and delayed drainage of the low‐permeability fractured matrix after recharge events. There are a number of different modeling approaches for the simulation of the karst groundwater dynamics, applicable to different aquifer as well as modeling problem types, ranging from continuum models to double continuum models to discrete and hybrid models. This study presents the application of an equivalent porous model approach (EPM, single continuum model) to construct a steady‐state numerical flow model for an important karst aquifer, that is, the Western Mountain Aquifer Basin (WMAB), shared by Israel and the West‐Bank, using MODFLOW2000. The WMAB was used as a catchment since it is a well‐constrained catchment with well‐defined recharge and discharge components and therefore allows a control on the modeling approach, a very rare opportunity for karst aquifer modeling. The model demonstrates the applicability of equivalent porous medium models for the simulation of karst systems, despite their large contrast in hydraulic conductivities. As long as the simulated saturated volume is large enough to average out the local influence of karst conduits and as long as transport velocities are not an issue, EPM models excellently simulate the observed head distribution. The model serves as a starting basis that will be used as a reference for developing a long‐term dynamic model for the WMAB, starting from the pre‐development period (i.e., 1940s) up to date.     

A geomorphology‐based integrated stream–aquifer interaction model for semi‐gauged catchments

Many of the existing stream–aquifer interaction models available in the literature are very complex with limited applicability in semi‐gauged and ungauged catchments. In this study, to estimate the influent and effluent subsurface water fluxes under limited geo‐hydrometeorological data availability conditions, a simple stream–aquifer interaction model, namely, the variable parameter McCarthy–Muskingum (VPMM) hillslope‐storage Boussinesq (hsB) model, has been developed. This novel model couples the VPMM streamflow transport with the hsB groundwater flow transport modules in online mode. In this integrated model, the surface water–groundwater flux exchange process is modelled by the Darcian approach with the variable hydraulic heads between the river stage and groundwater table accounting for the rainfall forcing. Considering the exchange fluxes in the hyporheic zone and lateral overland flow contribution, this approach is field tested in a typical 48‐km stretch of the Brahmani River in eastern India to simulate the streamflow and its depth with the minimum Nash–Sutcliffe efficiency of 94% and 88%; the maximum root mean square error of 134 m³/s and 0.35 m; and the minimum index of agreement of 98% and 97%, respectively. This modelling approach could be very well utilized in data‐scarce world‐river basins to estimate the stream–aquifer exchange flux due to rainfall forcings.     

An Open,Object-Based Framework for Generating Anisotropy in Sedimentary Subsurface Models

The spatial distribution of hydraulic properties in the subsurface controls groundwater flow and solute transport. However, many approaches to modeling these distributions do not produce geologically realistic results and/or do not model the anisotropy of hydraulic conductivity caused by bedding structures in sedimentary deposits. We have developed a flexible object-based package for simulating hydraulic properties in the subsurface—the Hydrogeological Virtual Realities (HyVR) simulation package. This implements a hierarchical modeling framework that takes into account geological rules about stratigraphic bounding surfaces and the geometry of specific sedimentary structures to generate realistic aquifer models, including full hydraulic-conductivity tensors. The HyVR simulation package can create outputs suitable for standard groundwater modeling tools (e.g., MODFLOW), is written in Python, an open-source programming language, and is openly available at an online repository. This paper presents an overview of the underlying modeling principles and computational methods, as well as an example simulation based on the Macrodispersion Experiment site in Columbus, Mississippi. Our simulation package can currently simulate porous media that mimic geological conceptual models in fluvial depositional environments, and that include fine-scale heterogeneity in distributed hydraulic parameter fields. The simulation results allow qualitative geological conceptual models to be converted into digital subsurface models that can be used in quantitative numerical flow-and-transport simulations, with the aim of improving our understanding of the influence of geological realism on groundwater flow and solute transport.     

RIPGIS-NET: a GIS tool for riparian groundwater evapotranspiration in MODFLOW

RIPGIS-NET, an Environmental System Research Institute (ESRI's) ArcGIS 9.2/9.3 custom application, was developed to derive parameters and visualize results of spatially explicit riparian groundwater evapotranspiration (ETg), evapotranspiration from saturated zone, in groundwater flow models for ecohydrology, riparian ecosystem management, and stream restoration. Specifically RIPGIS-NET works with riparian evapotranspiration (RIP-ET), a modeling package that works with the MODFLOW groundwater flow model. RIP-ET improves ETg simulations by using a set of eco-physiologically based ETg curves for plant functional subgroups (PFSGs), and separates ground evaporation and plant transpiration processes from the water table. The RIPGIS-NET program was developed in Visual Basic 2005, .NET framework 2.0, and runs in ArcMap 9.2 and 9.3 applications. RIPGIS-NET, a pre- and post-processor for RIP-ET, incorporates spatial variability of riparian vegetation and land surface elevation into ETg estimation in MODFLOW groundwater models. RIPGIS-NET derives RIP-ET input parameters including PFSG evapotranspiration curve parameters, fractional coverage areas of each PFSG in a MODFLOW cell, and average surface elevation per riparian vegetation polygon using a digital elevation model. RIPGIS-NET also provides visualization tools for modelers to create head maps, depth to water table (DTWT) maps, and plot DTWT for a PFSG in a polygon in the Geographic Information System based on MODFLOW simulation results.     

Bidirectional stream–groundwater flow in response to ephemeral and intermittent streamflow and groundwater seasonality

It is often assumed that the net groundwater flow direction is towards the channel in headwater streams in humid climates, with magnitudes dependent on flow state. However, studies that characterize stream–groundwater interactions in ephemeral and intermittent streams in humid landscapes remain sparse. Here, we examined seasonally driven stream–groundwater interactions in response to temporary streamflow on the basis of field observations of streamflow and groundwater on an adjacent hillslope. The direction of hydraulic head gradients between the stream and groundwater shifted seasonally. The stream gained water (head gradients were towards the stream) when storage state was high. During this period, streamflow was persistent. The stream lost water to the groundwater system (head gradients were away from the stream) when storage state was low. During this period, streamflow only occurred in response to precipitation events, and head gradients remained predominantly away from the stream during events. This suggested that mechanisms other than deep groundwater contributions produced run‐off when storage was low, such as surface and perched subsurface flowpaths above the water table. Analysis of the annual water balance for the study period showed that the residual between precipitation inputs and streamflow and evapotranspiration outputs, which were attributed to the loss of water to the deeper, regional groundwater system, was similar in magnitude to streamflow. This, coupled with results that showed bidirectionality in stream–groundwater head gradients, indicated that headwaters composed of temporary (e.g., ephemeral and intermittent) streams can be important focal areas for regional groundwater recharge, and both contribute to and receive water, solutes, and materials from the groundwater system.     

Integrated water resource management in a major canal command in eastern India

The present rice‐dominated cropping system in the Hirakud canal command (eastern India) is under severe threat due to imbalance between irrigation water supply and demand. The canal water supply, which is the only source of irrigation, only meets 54% of the demand at 90% probability of exceedance (PE). In order to mitigate the irrigation water deficit from canal water, groundwater is considered as a supplemental source. Quasi‐three‐dimensional groundwater flow simulation modelling was, therefore, carried out by using Visual MODFLOW to detect the change in hydraulic head due to transient pumping stresses. The simulation model was calibrated and validated satisfactorily. Sensitivity analysis of the model parameters shows that groundwater recharge is most sensitive followed by aquifer hydraulic conductivity at almost all the sites of the command area, whereas the model is comparatively less sensitive to specific storage and specific yield. Enhanced pumping scenarios showed that groundwater extraction can be increased up to 50 times of the existing pumping without causing any adverse effect to the aquifer but the aquifer does not permit to exploit water in order to fulfill the irrigation water demand even at 10% PE. Hence, it is imperative to develop an optimal land and water resources management plan of the command area. Copyright © 2011 John Wiley & Sons, Ltd.     

Estimating River Conductance from Prior Information to Improve Surface‐Subsurface Model Calibration

Most groundwater models simulate stream‐aquifer interactions with a head‐dependent flux boundary condition based on a river conductance (CRIV). CRIV is usually calibrated with other parameters by history matching. However, the inverse problem of groundwater models is often ill‐posed and individual model parameters are likely to be poorly constrained. Ill‐posedness can be addressed by Tikhonov regularization with prior knowledge on parameter values. The difficulty with a lumped parameter like CRIV, which cannot be measured in the field, is to find suitable initial and regularization values. Several formulations have been proposed for the estimation of CRIV from physical parameters. However, these methods are either too simple to provide a reliable estimate of CRIV, or too complex to be easily implemented by groundwater modelers. This paper addresses the issue with a flexible and operational tool based on a 2D numerical model in a local vertical cross section, where the river conductance is computed from selected geometric and hydrodynamic parameters. Contrary to other approaches, the grid size of the regional model and the anisotropy of the aquifer hydraulic conductivity are also taken into account. A global sensitivity analysis indicates the strong sensitivity of CRIV to these parameters. This enhancement for the prior estimation of CRIV is a step forward for the calibration and uncertainty analysis of surface‐subsurface models. It is especially useful for modeling objectives that require CRIV to be well known such as conjunctive surface water‐groundwater use.     

Aquifer Vulnerability Assessment Based on Sequence Stratigraphic and 39Ar Transport Modeling

A large‐scale groundwater flow and transport model is developed for a deep‐seated (100 to 300 m below ground surface) sedimentary aquifer system. The model is based on a three‐dimensional (3D) hydrostratigraphic model, building on a sequence stratigraphic approach. The flow model is calibrated against observations of hydraulic head and stream discharge while the credibility of the transport model is evaluated against measurements of ³⁹Ar from deep wells using alternative parameterizations of dispersivity and effective porosity. The directly simulated 3D mean age distributions and vertical fluxes are used to visualize the two‐dimensional (2D)/3D age and flux distribution along transects and at the top plane of individual aquifers. The simulation results are used to assess the vulnerability of the aquifer system that generally has been assumed to be protected by thick overlaying clayey units and therefore proposed as future reservoirs for drinking water supply. The results indicate that on a regional scale these deep‐seated aquifers are not as protected from modern surface water contamination as expected because significant leakage to the deeper aquifers occurs. The complex distribution of local and intermediate groundwater flow systems controlled by the distribution of the river network as well as the topographical variation (Tóth 1963) provides the possibility for modern water to be found in even the deepest aquifers.     

The influence of local hydrogeologic forcings on near‐stream event water recharge and retention (Upper San Pedro River,Arizona)

The rise in stream stage during high flow events (floods) can induce losing stream conditions, even along stream reaches that are gaining during baseflow conditions. The aquifer response to flood events can affect the geochemical composition of both near‐stream groundwater and post‐event streamflow, but the amount and persistence of recharged floodwater may differ as a function of local hydrogeologic forcings. As a result, this study focuses on how vertical flood recharge varies under different hydrogeologic forcings and the significance that recharge processes can have on groundwater and streamflow composition after floods. River and shallow groundwater samples were collected along three reaches of the Upper San Pedro River (Arizona, USA) before, during and after the 2009 and 2010 summer monsoon seasons. Tracer data from these samples indicate that subsurface floodwater propagation and residence times are strongly controlled by the direction and magnitude of the dominant stream–aquifer gradient. A reach that is typically strongly gaining shows minimal floodwater retention shortly after large events, whereas the moderately gaining and losing reaches can retain recharged floodwater from smaller events for longer periods. The moderately gaining reach likely returned flood recharge to the river as flow declined. These results indicate that reach‐scale differences in hydrogeologic forcing can control (i) the amount of local flood recharge during events and (ii) the duration of its subsurface retention and possible return to the stream during low‐flow periods. Our observations also suggest that the presence of floodwater in year‐round baseflow is not due to long‐term storage beneath the streambed along predominantly gaining reaches, so three alternative mechanisms are suggested: (i) repeated flooding that drives lateral redistribution of previously recharged floodwater, (ii) vertical recharge on the floodplain during overbank flow events and (iii) temporal variability in the stream–aquifer gradient due to seasonally varying water demands of riparian vegetation. Copyright © 2011 John Wiley & Sons, Ltd.     

Studies of a regulated dryland river: surface–groundwater interactions

Unlike rivers in humid regions, dryland rivers typically exhibit reduced flow in the downstream direction as a result of transmission losses, which include seepage of streamflow into the aquifer, evaporation, and transpiration. However, much remains to be learned about the nature of the exchange between surface water and groundwater in these landscapes, especially in terms of spatial and temporal variability. Our study focused on streambank seepage and groundwater flow in the alluvial aquifer, specifically on answering questions such as: Is there seasonal variability in seepage losses? Is seepage permanently lost? Can losses be reduced by killing riparian vegetation? To better understand the magnitude, variability, and fate of streambank seepage, we assessed river stages, groundwater hydraulic gradients, and groundwater flow paths at two sites along a reach of the Pecos River, a dryland perennial river in West Texas. We found that along this reach the river was losing water to the aquifer even under low‐flow conditions; but seepage was controlled by a number of different mechanisms. Seepage increased not only during high‐flow events but also when the groundwater level was declining owing to long periods of no irrigation release. Tamarix (saltcedar) control did not affect hydraulic gradients nor reduce streambank seepage and given that this reach of the Pecos River is a losing one, streamflow will not be enhanced by controlling saltcedar. These findings can be used to improve basic conceptual models of dryland river systems and to predict hydrologic responses to changes in the timing and magnitude of streamflows and to riparian vegetation management. Copyright © 2012 John Wiley & Sons, Ltd.     

Dynamic river–groundwater exchange in the presence of a saline,semi‐confined aquifer

Understanding groundwater–surface water exchange in river banks is crucial for effective water management and a range of scientific disciplines. While there has been much research on bank storage, many studies assume idealized aquifer systems. This paper presents a field‐based study of the Tambo Catchment (southeast Australia) where the Tambo River interacts with both an unconfined aquifer containing relatively young and fresh groundwater (<500 μS/cm and <100 years old) and a semi‐confined artesian aquifer containing old and saline groundwater (electrical conductivity > 2500 μS/cm and >10 000 years old). Continuous groundwater elevation and electrical conductivity monitoring within the different aquifers and the river suggest that the degree of mixing between the two aquifers and the river varies significantly in response to changing hydrological conditions. Numerical modelling using MODFLOW and the solute transport package MT3DMS indicates that saline water in the river bank moves away from the river during flooding as hydraulic gradients reverse. This water then returns during flood recession as baseflow hydraulic gradients are re‐established. Modelling also indicates that the concentration of a simulated conservative groundwater solute can increase for up to ~34 days at distances of 20 and 40 m from the river in response to flood events approximately 10 m in height. For the same flood event, simulated solute concentrations within 10 m of the river increase for only ~15 days as the infiltrating low‐salinity river water drives groundwater dilution. Average groundwater fluxes to the river stretch estimated using Darcy's law were 7 m³/m/day compared with 26 and 3 m³/m/day for the same periods via mass balance using Radon (²²²Rn) and chloride (Cl), respectively. The study shows that by coupling numerical modelling with continuous groundwater–surface water monitoring, the transient nature of bank storage can be evaluated, leading to a better understanding of the hydrological system and better interpretation of hydrochemical data. Copyright © 2015 John Wiley & Sons, Ltd.     

Modeling Variably Saturated Subsurface Solute Transport with MODFLOW‐UZF and MT3DMS

The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated‐zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume‐averaged approach in which Lagrangian‐based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF‐MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably‐Saturated Two‐Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two‐ and three‐dimensional simulations also were investigated to ensure unsaturated‐saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large‐scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF‐MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three‐dimensional variably saturated flow and transport simulations revealed UZF‐MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide‐spread use of both MODFLOW and MT3DMS, the added capability of unsaturated‐zone transport in this familiar modeling framework stands to benefit a broad user‐ship.