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Abstract. Surface water quality along river corridors can be modulated by hyporheic zones (HZs) that are ubiquitous and biogeochemically active. Watershed management practices often ignore the potentially important role of HZs as a natural reactor. To investigate the effect of hydrological exchange and biogeochemical processes on the fate of nutrients in surface water and HZs, a novel model, SWAT-MRMT-R, was developed coupling the Soil and Water Assessment Tool (SWAT) watershed model and the reaction module from a flow and reactive transport code (PFLOTRAN). SWAT-MRMT-R simulates concurrent nonlinear multicomponent biogeochemical reactions in both the channel water and its surrounding HZs, connecting the channel water and HZs through hyporheic exchanges using multirate mass transfer (MRMT) representation. Within the model, HZs are conceptualized as transient storage zones with distinguished exchange rates and residence times. The biogeochemical processes within HZs are different from those in the channel water. Hyporheic exchanges are modeled as multiple first-order mass transfers between the channel water and HZs. As a numerical example, SWAT-MRMT-R is applied to the Hanford Reach of the Columbia River, a large river in the United States, focusing on nitrate dynamics in the channel water. Major nitrate contaminants entering the Hanford Reach include those from the legacy waste, irrigation return flows (irrigation water that is not consumed by crops and runs off as point sources to the stream), and groundwater seepage resulting from irrigated agriculture. A two-step reaction sequence for denitrification and an aerobic respiration reaction is assumed to represent the biogeochemical transformations taking place within the HZs. The spatially variable hyporheic exchange rates and residence times in this example are estimated with the basin-scale Networks with EXchange and Subsurface Storage (NEXSS) model. Our simulation results show that (1), given a residence time distribution, how the exchange fluxes to HZs are approximated when using MRMT can significantly change the amount of nitrate consumption in HZs through denitrification and (2) source locations of nitrate have a different impact on surface water quality due to the spatially variable hyporheic exchanges.

The systematic response of coastal ecosystems to inundation and salinity exposure is fundamental to their ecology and biogeochemical function. Here we observe and model freshwater‐seawater interactions in a first‐order stream—floodplain system where tidal access was recently restored. Subsurface flow and transport modeling were used to quantify and better understand the interplay of processes, properties, and conditions that control water level and salinity in the floodplain to the tidal stream. Water levels in the stream were highly correlated with tidal forcing, which resulted in episodic inundation of the floodplain at quasi‐monthly frequency. The tidal stream is the only source of salinity to the floodplain, yet shallow groundwater salinity was considerably higher than average stream salinity. The low‐permeability clay floodplain soils limit lateral groundwater flow and transport, resulting in floodplain groundwater and salinity dynamics driven almost exclusively by infiltration during inundation events. As inundation occurs during high tide, estuarine waters reach the floodplain with minor attenuation in salinity from the stream's freshwater discharge. Infiltration and salinity exposure are topography controlled and regulated by ponding depth and duration, seasonal ground saturation, and depth to water table. The model suggests that floodplain salinity is currently in an early stage of transition from pre‐restoration freshwater conditions and will not reach equilibrium for ~20 years. These findings have broad relevance for understanding how and over what time scales coastal ecosystems will respond to increasing seawater exposure from sea level rise, ocean‐originating storms, and changes in natural and man‐made barriers.

The Amazon basin has experienced periodic droughts in the past, and intense and frequent droughts are predicted in the future. Landscape heterogeneity could play an important role in how tropical forests respond to drought by influencing water available to plants. Using the one‐dimensional ACME Land Model and the three‐dimensional ParFlow variably saturated flow model, numerical experiments were performed for a catchment in central Amazon to elucidate processes that influence water available for plant use and provide insights for improving Earth system models. Results from ParFlow show that topography has a dominant influence on groundwater table and runoff through lateral flow. Without any representations of lateral processes, ALM simulates very different seasonal variations in groundwater table and runoff compared to ParFlow even if it is able to reproduce the long‐term spatial average groundwater table of ParFlow through simple parameter calibration. In the ParFlow simulations, even in the plateau with much deeper water table depth during the dry season in the drought year of 2005, plant transpiration is not water stressed as the soil saturation is still sufficient for the stomata to be fully open based on the empirical wilting formulation in the models. This finding is insensitive to uncertainty in atmospheric forcing and soil parameters, but the empirical wilting formulation is an important factor that should be addressed using observations and modeling of coupled plant hydraulics‐soil hydrology processes in future studies. The results could be applicable to other catchments in the Amazon basin with similar seasonal variability and hydrologic regimes.

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