Migratory fishes with periodic life history strategies are sensitive to river regulation. Populations of these fishes may persist in highly regulated rivers by using tributaries that provide access to intermittently connected spawning and early life stage habitat in floodplains. We analyzed system hydrology and associated movement of a long-lived periodic strategist, the alligator gar ( Atractosteus spatula), in the Brazos River, Texas. We hypothesized that (1) flow regulation on the mainstem has resulted in the reduction of flood pulses, but tributaries have been less altered and (2) alligator gar migrate into tributaries during high flows and temperatures. Our analysis revealed that flood pulses were reduced in the mainstem but not in an adjacent, less regulated tributary where floodplain-inundating pulses now outnumber those in the mainstem. Using data from tagged fish, we derived statistical models predicting greater occurrence of alligator gar in tributaries when water temperature exceeded 25 C and mainstem discharge exceeded 400cubic meters per second. These results emphasize that movement into less regulated tributaries can mitigate impacts of river regulation on mainstem river populations of alligator gar.