[1] Hyporheic exchange flows were simulated using MODFLOW and MODPATH to estimate relative effects of channel morphologic features on the extent of the hyporheic zone, on hyporheic exchange flow, and on the residence time of stream water in the hyporheic zone. Four stream reaches were compared in order to examine the influence of stream size and channel constraint. Within stream reaches, the influence of pool-step or pool-riffle sequences, channel sinuosity, secondary channels, and channel splits was examined. Results showed that the way in which channel morphology controlled exchange flows differed with stream size and, in some cases, with channel constraint. Pool-step sequences drove hyporheic exchange in the second-order sites, creating exchange flows with relatively short residence times. Multiple features interacted to drive hyporheic exchange flow in the unconstrained fifth-order site, where pool-riffle sequences and a channel split created exchange flows with short residence times, whereas a secondary channel created exchange flows with long residence times. There was relatively little exchange flow in the bedrock-constrained fifth-order site. Groundwater flow models were effective in examining the morphologic features that controlled hyporheic exchange flow, and surface-visible channel morphologic features controlled the development of the hyporheic zone in these mountain streams.

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Stream restoration projects that aim to rehabilitate ecosystem health have not considered surface–subsurface linkages, although stream water and groundwater interaction has an important role in sustaining stream ecosystem functions. The present study examined the effect of constructed riffles and a step on hyporheic exchange flow and chemistry in restored reaches of several N-rich agricultural and urban streams in southern Ontario. Hydrometric data collected from a network of piezometers and conservative tracer releases indicated that the constructed riffles and steps were effective in inducing hyporheic exchange. However, despite the use of cobbles and boulders in the riffle construction, high stream dissolved oxygen (DO) concentrations were depleted rapidly with depth into the hyporheic zones. Differences between observed and predicted nitrate concentrations based on conservative ion concentration patterns indicated that these hyporheic zones were also nitrate sinks. Zones of low hydraulic conductivity and the occurrence of interstitial fines in the restored cobble-boulder layers suggest that siltation and clogging of the streambed may reduce the downwelling of oxygen- and nitrate-rich stream water. Increases in streambed DO levels and enhancement of habitat for hyporheic fauna that result from riffle–step construction projects may only be temporary in streams that receive increased sediment and nutrient inputs from urban areas and croplands.