We investigated spatial and temporal changes in subyearling fall Chinook salmon rearing habitat and areas dewatered below Bonneville Dam on the Columbia River. We used two-dimensional hydrodynamic modeling to predict water velocity and depth data. By combining two-dimensional hydrodynamic modeling with a predictive model of subyearling rearing presence, we were able to illustrate spatiotemporal changes in subyearling rearing areas, areas dewatered by flow reductions, and percentage of dewatered locations that were initially subyearling rearing areas. By using a geographic information system, we located areas of persistent subyearling rearing and areas frequently dewatered at 1-h change intervals from 1 April through 31 May, 2003. We validated predicted water velocities and surface elevations using empirically collected water velocities and surface elevations. We beach seined to collect subyearlings at random locations within the study area to validate predictions of subyearling presence.