In the Cook Inlet, a subarctic estuary in Alaska, the endangered population of beluga whales ( Delphinapterus leucas) has not recovered despite regulation of hunting and the reason is not well understood. To examine the potential roles of habitat and food availability, we compared spatial data on distribution and abundance from aerial surveys undertaken during the seasonal transition into early summer, with corresponding data for river discharge and salmon abundance. Principal component regression indicated strong relationships with rates of river discharge that explained over 90 % of the inter-annual variability of beluga abundances recorded in the Susitna Delta. Belugas moved away from the Susitna Delta when flow rate from the Susitna River was low relative to rivers draining into the Knik Arm and Turnagain Arm. Using only three principal components describing shape, river discharge during May explained 86 % of the inter-annual variability in abundances recorded in the Susitna Delta. In years of reduced abundance in the Susitna Delta, movement was toward the Knik Arm until 2003, transitioning thereafter to the Turnagain Arm including Chickaloon Bay. In contrast, escapements of Chinook salmon in the Deshka River (a tributary of the Susitna River) showed an inverse relationship with beluga abundance in the Susitna Delta, suggesting that escapements were dependent on beluga abundance. These results demonstrated the influence of highly dynamic habitat availability on the distribution of belugas and the importance of the physical environment in structuring the activity of higher predators on prey species. [ABSTRACT FROM AUTHOR]