SFRmaker and Linesink-Maker: Rapid Construction of Streamflow Routing Networks from Hydrography Data

Groundwater models have evolved to encompass more aspects of the water cycle, but the incorporation of realistic boundary conditions representing surface water remains time-consuming and error-prone. We present two Python packages that robustly automate this process using readily available hydrography data as the primary input. SFRmaker creates input for the MODFLOW SFR package, while Linesink-maker creates linesink string input for the GFLOW analytic element program. These programs can reduce weeks or even months of manual effort to a few minutes of execution time, and carry the added advantages of reduced potential for error, improved reproducibility and facilitation of step-wise modeling through reduced dependency on a particular conceptual model or discretization. Two real-world examples at the county to multi-state scales are presented.     

Spatial Periodic Boundary Condition for MODFLOW

Small‐scale hyporheic zone (HZ) models often use a spatial periodic boundary (SPB) pair to simulate an infinite repetition of bedforms. SPB's are common features of commercially available multiphysics modeling packages. MODFLOW's lack of this boundary type has precluded it from being effectively utilized in this area of HZ research. We present a method to implement the SPB in MODFLOW by development of the appropriate block‐centered finite‐difference expressions. The implementation is analogous to MODFLOW's general head boundary package. The difference is that the terms on the right hand side of the solution equations must be updated with each iteration. Consequently, models that implement the SPB converge best with solvers that perform both inner and outer iterations. The correct functioning of the SPB condition in MODFLOW is verified by two examples. This boundary condition allows users to build HZ‐bedform models in MODFLOW, facilitating further research using related codes such as MT3DMS and PHT3D.     

Field Test of a Hybrid Finite‐Difference and Analytic Element Regional Model

Regional finite‐difference models often have cell sizes that are too large to sufficiently model well‐stream interactions. Here, a steady‐state hybrid model is applied whereby the upper layer or layers of a coarse MODFLOW model are replaced by the analytic element model GFLOW, which represents surface waters and wells as line and point sinks. The two models are coupled by transferring cell‐by‐cell leakage obtained from the original MODFLOW model to the bottom of the GFLOW model. A real‐world test of the hybrid model approach is applied on a subdomain of an existing model of the Lake Michigan Basin. The original (coarse) MODFLOW model consists of six layers, the top four of which are aggregated into GFLOW as a single layer, while the bottom two layers remain part of MODFLOW in the hybrid model. The hybrid model and a refined “benchmark” MODFLOW model simulate similar baseflows. The hybrid and benchmark models also simulate similar baseflow reductions due to nearby pumping when the well is located within the layers represented by GFLOW. However, the benchmark model requires refinement of the model grid in the local area of interest, while the hybrid approach uses a gridless top layer and is thus unaffected by grid discretization errors. The hybrid approach is well suited to facilitate cost‐effective retrofitting of existing coarse grid MODFLOW models commonly used for regional studies because it leverages the strengths of both finite‐difference and analytic element methods for predictions in mildly heterogeneous systems that can be simulated with steady‐state conditions.     

Simulating ground water-lake interactions: approaches and insights

Approaches for modeling lake-ground water interactions have evolved significantly from early simulations that used fixed lake stages specified as constant head to sophisticated LAK packages for MODFLOW. Although model input can be complex, the LAK package capabilities and output are superior to methods that rely on a fixed lake stage and compare well to other simple methods where lake stage can be calculated. Regardless of the approach, guidelines presented here for model grid size, location of three-dimensional flow, and extent of vertical capture can facilitate the construction of appropriately detailed models that simulate important lake-ground water interactions without adding unnecessary complexity. In addition to MODFLOW approaches, lake simulation has been formulated in terms of analytic elements. The analytic element lake package had acceptable agreement with a published LAKI problem, even though there were differences in the total lake conductance and number of layers used in the two models. The grid size used in the original LAKI problem, however, violated a grid size guideline presented in this paper. Grid sensitivity analyses demonstrated that an appreciable discrepancy in the distribution of stream and lake flux was related to the large grid size used in the original LAKI problem. This artifact is expected regardless of MODFLOW LAK package used. When the grid size was reduced, a finite-difference formulation approached the analytic element results. These insights and guidelines can help ensure that the proper lake simulation tool is being selected and applied.     

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.     

Modeling Steady Sea Water Intrusion with Single‐Density Groundwater Codes

Steady interface flow in heterogeneous aquifer systems is simulated with single‐density groundwater codes by using transformed values for the hydraulic conductivity and thickness of the aquifers and aquitards. For example, unconfined interface flow may be simulated with a transformed model by setting the base of the aquifer to sea level and by multiplying the hydraulic conductivity with 41 (for sea water density of 1025 kg/m³). Similar transformations are derived for unconfined interface flow with a finite aquifer base and for confined multi‐aquifer interface flow. The head and flow distribution are identical in the transformed and original model domains. The location of the interface is obtained through application of the Ghyben‐Herzberg formula. The transformed problem may be solved with a single‐density code that is able to simulate unconfined flow where the saturated thickness is a linear function of the head and, depending on the boundary conditions, the code needs to be able to simulate dry cells where the saturated thickness is zero. For multi‐aquifer interface flow, an additional requirement is that the code must be able to handle vertical leakage in situations where flow in an aquifer is unconfined while there is also flow in the aquifer directly above it. Specific examples and limitations are discussed for the application of the approach with MODFLOW. Comparisons between exact interface flow solutions and MODFLOW solutions of the transformed model domain show good agreement. The presented approach is an efficient alternative to running transient sea water intrusion models until steady state is reached.     

Developing Potentiometric Surfaces and Flow Fields with a Head‐Specified MODFLOW Model

Investigating changes in an aquifer system often involves comparison of observed heads from different synoptic measurements, generally with potentiometric surfaces developed by hand or a statistical approach. Alternatively, head‐specified MODFLOW models, in which constant head cells simulate observed heads, generate gridded potentiometric surfaces that explicitly account for Darcy's Law and mass balance. We developed a transient head‐specified MODFLOW model for the stratified Cambrian‐Ordovician sandstone aquifer system of northeastern Illinois to analyze flow within its 275 m deep cone of depression. Potentiometric surfaces were developed using static heads from production wells regardless of open interval; hence assuming no vertical head difference. This assumption was tested against steady‐state, head‐specified models of each sandstone strata for 1980 and 2014. The results indicate that the original conceptual model was appropriate in 1980 but not 2014, where a vertical head difference had developed at the center of the cone of depression. For earlier years, when the head difference was minimal, the transient head‐specified model compared well with a traditional, flow‐specified model. In later years, the transient head‐specified model overestimated removal of water from storage. MODFLOW facilitates the development of a time‐series of potentiometric surfaces and can easily be modified to test the impacts of different conceptual models, such as assumptions on vertical head differences. For this study of a deep confined aquifer, MODFLOW also offers advantages in generating potentiometric surfaces and flow fields over statistical interpolation techniques, although future research is needed to assess its performance in other settings.     

Unstructured Gridding for MODFLOW from Prior Groundwater Flow Models: A New Paradigm

This work introduces a new unstructured gridding approach relying on feedback from a previous groundwater flow model. All cells in a relatively coarse model using a rectilinear grid are recursively subdivided following a cell wise specific discharge-based indicator to generate quadtree, octree or Voronoï grids. This technique leverages the full potential of the latest MODFLOW engines. The suitability of this approach is demonstrated on challenging single and multilayered heterogeneous formations. The proposed method is straightforward to implement in existing software packages. It supports iterative updating of groundwater flow models from the legacy rectilinear to unstructured grids.     

Effect of elevation resolution on evapotranspiration simulations using MODFLOW

Surface elevations represented in MODFLOW head-dependent packages are usually derived from digital elevation models (DEMs) that are available at much high resolution. Conventional grid refinement techniques to simulate the model at DEM resolution increases computational time, input file size, and in many cases are not feasible for regional applications. This research aims at utilizing the increasingly available high resolution DEMs for effective simulation of evapotranspiration (ET) in MODFLOW as an alternative to grid refinement techniques. The source code of the evapotranspiration package is modified by considering for a fixed MODFLOW grid resolution and for different DEM resolutions, the effect of variability in elevation data on ET estimates. Piezometric head at each DEM cell location is corrected by considering the gradient along row and column directions. Applicability of the research is tested for the lower Rio Grande (LRG) Basin in southern New Mexico. The DEM at 10 m resolution is aggregated to resampled DEM grid resolutions which are integer multiples of MODFLOW grid resolution. Cumulative outflows and ET rates are compared at different coarse resolution grids. Results of the analysis conclude that variability in depth-to-groundwater within the MODFLOW cell is a major contributing parameter to ET outflows in shallow groundwater regions. DEM aggregation methods for the LRG Basin have resulted in decreased volumetric outflow due to the formation of a smoothing error, which lowered the position of water table to a level below the extinction depth.     

MODFLOW as a Configurable Multi-Model Hydrologic Simulator

MODFLOW 6 is the latest in a line of six “core” versions of MODFLOW released by the U.S. Geological Survey. The MODFLOW 6 architecture supports incorporation of additional hydrologic processes, in addition to groundwater flow, and allows interaction between processes. The architecture supports multiple model instances and multiple types of models within a single simulation, a flexible approach to formulating and solving the equations that represent hydrologic processes, and recent advances in interoperability, which allow MODFLOW to be accessed and controlled by external programs. The present version of MODFLOW 6 consolidates popular capabilities available in MODFLOW variants, such as the unstructured grid support in MODFLOW-USG, the Newton-Raphson formulation in MODFLOW-NWT, and the support for partitioned stress boundaries in MODFLOW-CDSS. The flexible multi-model capability allows users to configure MODFLOW 6 simulations to represent the local-grid refinement (LGR) capabilities available in MODFLOW-LGR, the multi-species transport capabilities in MT3DMS, and the coupled variable-density capabilities available in SEAWAT. This paper provides a new, holistic and integrated overview of simulation capabilities made possible by the MODFLOW 6 architecture, and describes how ongoing and future development can take advantage of the program architecture to integrate new capabilities in a way that is minimally invasive and automatically compatible with the existing MODFLOW 6 code.     

A Semi‐Structured MODFLOW‐USG Model to Evaluate Local Water Sources to Wells for Decision Support

In order to better represent the configuration of the stream network and simulate local groundwater‐surface water interactions, a version of MODFLOW with refined spacing in the topmost layer was applied to a Lake Michigan Basin (LMB) regional groundwater‐flow model developed by the U.S. Geological. Regional MODFLOW models commonly use coarse grids over large areas; this coarse spacing precludes model application to local management issues (e.g., surface‐water depletion by wells) without recourse to labor‐intensive inset models. Implementation of an unstructured formulation within the MODFLOW framework (MODFLOW‐USG) allows application of regional models to address local problems. A “semi‐structured” approach (uniform lateral spacing within layers, different lateral spacing among layers) was tested using the LMB regional model. The parent 20‐layer model with uniform 5000‐foot (1524‐m) lateral spacing was converted to 4 layers with 500‐foot (152‐m) spacing in the top glacial (Quaternary) layer, where surface water features are located, overlying coarser resolution layers representing deeper deposits. This semi‐structured version of the LMB model reproduces regional flow conditions, whereas the finer resolution in the top layer improves the accuracy of the simulated response of surface water to shallow wells. One application of the semi‐structured LMB model is to provide statistical measures of the correlation between modeled inputs and the simulated amount of water that wells derive from local surface water. The relations identified in this paper serve as the basis for metamodels to predict (with uncertainty) surface‐water depletion in response to shallow pumping within and potentially beyond the modeled area, see Fienen et al. (2015a).     

IHMS—Integrated Hydrological Modelling System. Part 1. Hydrological processes and general structure

A newly Integrated Hydrological Modelling System (IHMS) has been developed to study the impact of changes in climate, land use and water management on groundwater and seawater intrusion (SWI) into coastal areas. The system represents the combination of three models, which can, if required, be run separately. It has been designed to assess the combined impact of climate, land use and groundwater abstraction changes on river, drainage and groundwater flows, groundwater levels and, where appropriate, SWI. The approach is interdisciplinary and reflects an integrated water management approach. The system comprises three packages: the Distributed Catchment Scale Model (DiCaSM), MODFLOW (96 and 2000) and SWI models. In addition to estimating all water balance components, DiCaSM, produces the recharge data that are used as input to the groundwater flow model of the US Geological Survey, MODFLOW. The latter subsequently generates the head distribution and groundwater flows that are used as input to the SWI model, SWI. Thus, any changes in land use, rainfall, water management, abstraction, etc. at the surface are first handled by DiCaSM, then by MODFLOW and finally by the SWI. The three models operate at different spatial and temporal scales and a facility (interface utilities between models) to aggregate/disaggregate input/output data to meet a desired spatial and temporal scale was developed allowing smooth and easy communication between the three models. As MODFLOW and SWI are published and in the public domain, this article focuses on DiCaSM, the newly developed unsaturated zone DiCaSM and equally important the interfacing utilities between the three models. DiCaSM simulates a number of hydrological processes: rainfall interception, evapotranspiration, surface runoff, infiltration, soil water movement in the root zone, plant water uptake, crop growth, stream flow and groundwater recharge. Input requirements include distributed data sets of rainfall, land use, soil types and digital terrain; climate data input can be either distributed or non‐distributed. The model produces distributed and time series output of all water balance components including potential evapotranspiration, actual evapotranspiration, rainfall interception, infiltration, plant water uptake, transpiration, soil water content, soil moisture (SM) deficit, groundwater recharge rate, stream flow and surface runoff. This article focuses on details of the hydrological processes and the various equations used in DiCaSM, as well as the nature of the interface to the MODFLOW and SWI models. Furthermore, the results of preliminary tests of DiCaSM are reported; these include tests related to the ability of the model to predict the SM content of surface and subsurface soil layers, as well as groundwater levels. The latter demonstrates how the groundwater recharge calculated from DiCaSM can be used as input into the groundwater model MODFLOW using aggregation and disaggregation algorithms (built into the interface utility). SWI has also been run successfully with hypothetical examples and was able to reproduce the results of some of the original examples of Bakker and Schaars ( 2005 ). In the subsequent articles, the results of applications to different catchments will be reported. Copyright © 2010 John Wiley & Sons, Ltd.     

Discontinuous Steady‐State Analytical Solutions of the Boussinesq Equation and Their Numerical Representation by Modflow

Known analytical solutions of groundwater flow equations are routinely used for verification of computer codes. However, these analytical solutions (e.g., the Dupuit solution for the steady‐state unconfined unidirectional flow in a uniform aquifer with a flat bottom) represent smooth and continuous water table configurations, simulating which does not pose any significant problems for the numerical groundwater flow models, like MODFLOW. One of the most challenging numerical cases for MODFLOW arises from drying‐rewetting problems often associated with abrupt changes in the elevations of impervious base of a thin unconfined aquifer. Numerical solutions of groundwater flow equations cannot be rigorously verified for such cases due to the lack of corresponding exact analytical solutions. Analytical solutions of the steady‐state Boussinesq equation, associated with the discontinuous water table configurations over a stairway impervious base, are presented in this article. Conditions resulting in such configurations are analyzed and discussed. These solutions appear to be well suited for testing and verification of computer codes. Numerical solutions, obtained by the latest versions of MODFLOW (MODFLOW‐2005 and MODFLOW‐NWT), are compared with the presented discontinuous analytical solutions. It is shown that standard MODFLOW‐2005 code (as well as MODFLOW‐2000 and older versions) has significant convergence problems simulating such cases. The problems manifest themselves either in a total convergence failure or erroneous results. Alternatively, MODFLOW‐NWT, providing a good match to the presented discontinuous analytical solutions, appears to be a more reliable and appropriate code for simulating abrupt changes in water table elevations.     

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 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.     

Efficient Storage of Large MODFLOW Models

We present a methodology for storing the bulkier portions of a set of MODFLOW input and output files in a compressed binary format using the HDF5 library. This approach results in compression ratios of up to 99% with no significant time penalty. The highly compressed format is particularly beneficial when dealing with large regional models or Monte Carlo simulations. The strategy is focused on the list‐ and array‐based portions of the input files including the cell property and recharge arrays, and is compatible with models containing parameters, including pilot points. The utilities are based on a modified version of the MODFLOW code and are, therefore, compatible with any standard MODFLOW simulation. We present used cases and instructions on how to use the utilities.     

Integrated modeling as a decision‐aiding tool for groundwater management in a Mediterranean agricultural watershed

A decision‐aiding methodology for agricultural groundwater management is presented; it is based on the combination of a watershed model, a groundwater flow model, and an optimization model. This methodology was applied to an agricultural watershed in northeastern Greece. The watershed model used was the Soil and Water Assessment Tool (SWAT), which provided recharge rates for the aquifers. These recharge rates were imported in the well‐known MODFLOW groundwater flow model. Both models were calibrated and verified using field data. Then, the nonlinear optimization problem was solved by a piecewise linearization process, in which the Simplex algorithm was applied sequentially. Apart from several pumping and climate change sensitivity scenarios, a land use change scenario and a climate change scenario, combining the three models, were tested, showing the ability of this methodology to be used in the decision‐making process. Copyright © 2012 John Wiley & Sons, Ltd.     

Simulating Piecewise-Linear Surface Water and Ground Water Interactions with MODFLOW

The standard MODFLOW packages offer limited capabilities to model piecewise-linear boundary conditions to describe ground water–surface water interaction. Specifically, MODFLOW is incapable of representing a Cauchy-type boundary with different resistances for discharge or recharge conditions. Such a more sophisticated Cauchy boundary condition is needed to properly represent surface waters alternatively losing water through the bottom (high resistance) or gaining water mostly near the water surface (low resistance). One solution would be to create a new package for MODFLOW to accomplish this. However, it is also possible to combine multiple instances of standard packages in a single cell to the same effect. In this specific example, the general head boundary package is combined with the drain package to arrive at the desired piecewise-linear behavior. In doing so, the standard USGS MODFLOW version can be used without any modifications at the expense of a minor increase in preprocessing and postprocessing and computational effort. The extra preprocessing for creating the input and extra postprocessing to determine the water balance in terms of the physical entities from the MODFLOW cell fluxes per package can be taken care of by a user interface.     

Contamination Assessment and Site-Management Tool (CAST): A Browser-Based Tool for Site Assessment

Groundwater dependency is increasing globally, while millions of potentially contaminated sites are yet to be characterized for contamination levels. In particular, groundwater contamination due to light nonaqueous phase liquids (LNAPLs) continues to be a global challenge. Mathematical approaches (i.e., analytical, semi-analytical, empirical, numerical) are preferred for an initial site assessment to circumvent the high characterization costs and limited site data availability. However, the site-specific nature of contamination restricts the generalization of any single approach. Hence, the requirement is for an easy-to-use computing interface that provides site-specific data management, the selection and use of multiple-model interfaces for computing, and site characterization, with extension for the latest models as they become available. This work provides one such interface called CAST or Contamination Assessment and Site-management Tool. CAST is an open-source browser-based (online/offline) tool that provides an interface for six different analytical models (e.g., BIOSCREEN-AT), a MODFLOW based numerical model, and two empirical models (including a hybrid numerical-analytical model). Additionally, CAST includes interfaces for site data management, their evaluation, and scenario-based modeling. CAST's development is in a modular format, which simplifies the addition of new computing or data interfaces. Furthermore, the entire code-base of CAST is based on open-source (dominantly Python programming) libraries and standards. This further simplifies the modification or extension of this tool. This paper introduces CAST, its different computing, and data management interfaces and provides examples of the tool's functionality primarily for the initial evaluation of contaminated sites.