The timing of life history events in many plants and animals depends on the seasonal fluctuations of specific environmental conditions. Climate change is altering environmental regimes and disrupting natural cycles and patterns across communities. Anadromous fishes that migrate between marine and freshwater habitats to spawn are particularly sensitive to shifting environmental conditions and thus are vulnerable to the effects of climate change. However, for many anadromous fish species the specific environmental mechanisms driving migration and spawning patterns are not well understood. In this study, we investigated the upstream spawning migrations of river herring Alosa spp. in 12 coastal Massachusetts streams. By analyzing long-term data sets (8–28 years) of daily fish counts, we determined the local influence of environmental factors on daily migration patterns and compared seasonal run dynamics and environmental regimes among streams. Our results suggest that water temperature was the most consistent predictor of both daily river herring presence–absence and abundance during migration. We found inconsistent effects of streamflow and lunar phase, likely due to the anthropogenic manipulation of flow and connectivity in different systems. Geographic patterns in run dynamics and thermal regimes suggest that the more northerly runs in this region are relatively vulnerable to climate change due to migration occurring later in the spring season, at warmer water temperatures that approach thermal maxima, and during a narrower temporal window compared to southern runs. The phenology of river herring and their reliance on seasonal temperature patterns indicate that populations of these species may benefit from management practices that reduce within-stream anthropogenic water temperature manipulations and maintain coolwater thermal refugia.