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Salinity can have major detrimental impacts on soil health, crop yield, and environmental ecosystem services. In this paper we introduce SWAT-MODFLOW-Salt, a version of SWAT-MODFLOW that simulates the fate and transport of major salt ions (SO 4 2−, Cl−, CO 3 2−, HCO 3 −, Ca2+, Na+, Mg2+, K+) in watershed systems, and focus on its development and application to irrigated stream-aquifer systems. The modeling code accounts for water and salt mass storage in soils, aquifer, and streams, and the movement of water and salt mass in surface runoff, soil lateral flow, percolation and recharge, groundwater flow, and groundwater-surface water exchange. The model is applied to a highly managed, irrigated 700 km2 region of the saline Lower Arkansas River Valley in Colorado, USA. The model is tested against groundwater salt concentrations and in-stream salt mass loadings, and then used to quantify the impact of soil salinity on crop yield. • We provide a new version of SWAT-MODFLOW that simulates salt ion transport in watershed systems • Salt ions are subject to all major hydrologic fluxes and precipitation-dissolution of salt minerals • The SWAT-MODFLOW-Salt code is applied to a saline stream-aquifer system in Colorado • The model can be used for salinity management scenario analysis [ABSTRACT FROM AUTHOR]

Waterlogging on croplands has been a known problem for a long time, leading to adverse social, physical, economic and environmental issues. To better solve the problem, the complicated plant-soil-water dynamics system needs to be better understood. The challenge is to simulate the interactions between the components in the systems. There are models that simulate plant-soil-water system but either run the processes independently leading to inaccuracy or has high invasiveness of using integrated models. This paper presents a tightly coupled model, DayCent-MODFLOW, that links a 3D ground-water flow (MODFLOW) model and a 1D agroecosystem model (DayCent). DayCent is responsible for plant-soil-water dynamic in the root zone, whereas MODFLOW simulates head and groundwater flow in the saturated zone of the aquifer. DayCent passes deep percolation from the soil profile to the water table and, under conditions of waterlogging in which the water table is within the soil profile, DayCent soil hydrologic processes are constrained by the presence of the water table simulated by MODFLOW. The coupling is achieved by adopting a parallel inter-process communication technique MPI (Message Passing Interface). The model is applied to a waterlogged agricultural area (22 km2) in northern Colorado, USA and tested against groundwater head and rates of evapotranspiration (ET). The model runs in parallel with multiple processes on the largest AWS Linux server. Groundwater heads match measured heads to a reasonable degree, and ET rates match reference ET and are highly correlated with crop type. Results show the strong hydrologic interaction between the two models. Greenhouse gas emissions from soil (N 2 O and CH 4) were also estimated by the model under the waterlogged conditions. Although the model can be used to simulate any plant-soil-aquifer system, no matter the depth of the water table, results from this study show that the model can be used to assess crop productivity, recharge, ET, and greenhouse gas emissions in areas of shallow groundwater. • A new hydro-agronomic model is introduced by integrating the MODFLOW groundwater flow model and the DayCent 1D agronomic model. • The crop-soil-water dynamics are better simulated in the waterlogged areas using the coupled model. • MPI is utilized as communication tool for the coupling models to decrease overall run time and minimize code invasiveness. • The model can assess recharge, and gas emissions under deep and shallow water table conditions in agricultural areas. [ABSTRACT FROM AUTHOR]

APEX (A gricultural P olicy/ E nvironmental e X tender) is an oft-used agroecosystem model but has limited use in groundwater-driven watersheds due to a simplistic representation of groundwater processes. This paper presents the linkage of APEX and the groundwater flow model MODFLOW into a single modeling code. The mapping of recharge, groundwater head, and groundwater-surface water interactions are handled internally via subroutines. The APEX-MODFLOW model is applied to three watersheds in the United States for testing code accuracy and hydrologic state variables and fluxes: the Animas River Watershed, Colorado and New Mexico (3543 km2); the Price River Watershed, Utah (4886 km2); and the Middle Bosque River Watershed, Texas (470 km2). Whereas the hydrology of the Animas River and Price River watersheds is driven by snowmelt and spring runoff, the hydrology of the Middle Bosque River Watershed is driven by summer thunderstorms. The model can be used for scenario analysis in groundwater-driven watersheds. • New integrated hydrologic model links APEX model to MODFLOW model. • Model passes recharge, water table elevation, and gw-sw flux rates internally. • APEX-MODFLOW applied to three watersheds in Utah, Colorado, and Texas, USA. • Model results show importance of including physically based groundwater flow. [ABSTRACT FROM AUTHOR]