A two-dimensional hydrodynamic model was applied to seven study reaches in the Colorado River within Grand Canyon to examine how operation of Glen Canyon Dam has affected availability of suitable shoreline habitat and dispersal of juvenile humpback chub (Gila cypha). Suitable shoreline habitat typically declined with increasing discharges above 226-425 m3/s, although the response varied among modelled reaches and was strongly dependent on local morphology. The area of suitable shoreline habitat over cover types that are preferred by juvenile humpback chub, however, stayed constant, and in some reaches, actually increased with discharge. In general, changes in discharge caused by impoundment tended to decrease availability of suitable shoreline habitat from September to February, but increased habitat availability in spring (May-June). Hourly variation in discharge from Glen Canyon Dam substantially reduced the amount of persistent shoreline habitat at all reaches. Changes in suitable shoreline habitat with discharge were shown to potentially bias historical catch per unit effort indices of native fish abundance up to fourfold. Physical retention of randomly placed particles simulating the movement of juvenile humpback chub in the study reaches tended to decline with increasing discharge, but the pattern varied considerably due to differences in the local morphology among reaches and the type of swimming behaviour modelled. Implications of these results to current hypotheses about the effects of Glen Canyon Dam on juvenile humpback chub survival in the mainstern Colorado River are discussed. ?? 2004 John Wiley and Sons, Ltd.