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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) lowkandH > 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.

Riparian zones are key gateways for solutes in watersheds, including nutrients and pollutants moving toward the stream network. In human‐dominated landscapes, they are widely used as buffers to remove pollutants at substantial cumulative cost yet vary widely in their effectiveness, and much is unknown about the detailed processes involved and their controls. Preferential flow is widespread in riparian zones, oriented both horizontally toward the channel (often bypassing beneficial reactions in the soil during baseflow) or vertically (enhancing beneficial reactions by infiltrating surface flow during storms). Preferential flow thus contributes to widespread variability of riparian zone/buffer function, with implications for legacy nutrients stored in upland soils and aquifers. This creates a disconnect between functional riparian definitions based on flow and transport processes and common operational ones based on buffer width. Enhanced field characterization of preferential flow path spatial distribution and connectivity, together with developments in simulating preferential solute transport in soils, would allow better prediction of spatial and temporal variation in riparian zone function. Such prediction in turn would allow improved buffer function by tailoring buffer design to site specific conditions, thereby reconciling functional and operational viewpoints.

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.

Restoring hydrologic connectivity between channels and floodplains is common practice in stream and river restoration. Floodplain hydrology and hydrogeology impact stream hydraulics, ecology, biogeochemical processing, and pollutant removal, yet rigorous field evaluations of surface water–groundwater exchange within floodplains during overbank floods are rare. We conducted five sets of experimental floods to mimic floodplain reconnection by pumping stream water onto an existing floodplain swale. Floods were conducted throughout the year to capture seasonal variation and each involved two replicate floods on successive days to test the effect of varying antecedent moisture. Water levels and specific conductance were measured in surface water, soil, and groundwater within the floodplain, along with surface flow into and out of the floodplain. Vegetation density varied seasonally and controlled the volume of surface water storage on the floodplain. By contrast, antecedent moisture conditions controlled storage of water in floodplain soils, with drier antecedent moisture conditions leading to increased subsurface storage and slower flood wave propagation across the floodplain surface. The site experienced spatial heterogeneity in vertical connectivity between surface water and groundwater across the floodplain surface, where propagation of hydrostatic pressure, preferential flow, and bulk Darcy flow were all mechanisms that may have occurred during the five floods. Vertical connectivity also increased with time, suggesting higher frequency of floodplain inundation may increase surface water–groundwater exchange across the floodplain surface. Understanding the variability of floodplain impacts on water quality noted in the literature likely requires better accounting for seasonal variations in floodplain vegetation and antecedent moisture as well as heterogeneous exchange flow mechanisms. Copyright © 2016 John Wiley & Sons, Ltd.