The hyporheic zone is the ecotone between stream and river channel flow and groundwater that can process nutrients and improve water quality. Transient hyporheic zones occur in the riparian zone (bank storage or “lung model” exchange) during channel stage fluctuations. Recent studies show that soil pipes are widespread in stream banks and beneath floodplains, creating highly preferential flow between channel and riparian groundwater such that the traditional Darcy model of flow does not apply. We used MODFLOW with the conduit flow package to model a series of stream bank soil pipes and examined soil pipe density (number per m), length, diameter, height above baseflow water surface, connectivity, and matrix hydraulic conductivity on transient particle flow paths and total hyporheic exchange volume (i.e., bank storage) over the course of a peak flow (e.g., storm) event. We found that adding five soil pipes per meter more than doubled hyporheic volume. Soil pipe length was the most important control; adding one 1.5‐m‐long soil pipe caused a 73.4% increase in hyporheic volume. The effect of increasing soil pipe diameter on hyporheic volume leveled off at ~1 cm, as flow limitation switched from pipe flow to pipe‐matrix exchange. To validate our approach, we used the model to successfully reproduce trends from field studies. Our results highlight the need to consider soil pipes when modeling, monitoring, or managing bank storage, floodplain connectivity, or hyporheic exchange.

Peak flow events in gaining stream/river channels cause lung model hyporheic exchange with the banks (bank storage), which fosters beneficial reactions as polluted channel water cycles through riparian groundwater. Soil pipes are common along stream/riverbanks, and enhance exchange, yet their effect on reactions such as denitrification is unknown. We used MODFLOW with the Conduit Flow Package to simulate lung model exchange during a peak flow event in a section of stream bank/riparian soil with soil pipes, and MT3D‐USGS to estimate nitrate transport and denitrification. We varied soil matrix hydraulic conductivity (K) and first‐order reaction constant (k), as well as soil pipe density, length, and height above the initial channel water surface elevation (H). The addition of soil pipes enhanced stream bank (riparian) denitrification relative to banks without pipes, e.g., a 76% increase due to adding a single 1.5 m pipe. Denitrification increased linearly with pipe density but exhibited nonlinear trends with other parameters. Sensitivity analysis revealed length and density to be most influential. Soil pipe enhancement of denitrification was governed by hyporheic volume in most cases in our study. Exceptions included (a) coarse soil (K = 10−3 m/s) and (b) low k and H > 0. Scaling our results to the stream corridor scale estimated that five soil pipes per m cumulatively induced 3% nitrate removal along a 1 km reach. Overall, soil pipes enhanced advection of nitrate into the banks, and also increased residence times of that nitrate under certain conditions, which together enhanced denitrification. This enhancement has implications for excess nitrate management in watersheds.

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