Human activities have degraded riparian systems in numerous ways, including homogenization of the floodplain landscape and minimization of extreme flows. We analyzed the effects of changes in these and other factors for extinction-colonization dynamics of a threatened Bank Swallow population along the upper Sacramento River, California, U.S.A. We monitored Bank Swallow distributions along a 160-km stretch of the river from 1986-1992 and 1996-2003 and tested whether site extinctions and colonizations corresponded with changes in maximum river discharge, surrounding land cover, estimated colony size, temperature, and precipitation. Colonization probabilities increased with maximum discharge. Extinction probabilities decreased with proximity to the nearest grassland, decreased with colony size, and increased with maximum discharge. To explore the implications for restoration, we incorporated the statistically estimated effects of distance to grassland and maximum discharge into simple metapopulation models. Under current conditions, the Bank Swallow metapopulation appears to be in continued decline, although stable or increasing numbers cannot be ruled out with the existing data. Maximum likelihood parameters from these regression models suggest that the Sacramento River metapopulation could be restored to 45 colonies through moderate amounts of grassland restoration, large increases in discharge, or direct restoration of nesting habitat by removing approximately 10% of existing bank protection (riprap) from suitable areas. Our results highlight the importance of grassland restoration, mixed benefits of restoring high spring discharge, and the importance of within-colony dynamics as areas for future research.