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.