The long-lived migratory fish in the lower Athabasca region (including the Athabasca oil sands region) are valued ecosystem components and good bio-indicators of changes in habitat condition, water quality and quantity over the entire stream network. Changes in this region may have been caused by a variety of human activities including oil sands development, forestry, urban development, and recreational activities. We reviewed existing data to examine whether community composition and health of migratory fish (such as northern pike, walleye, and suckers) in the lower Athabasca region have changed over the past 40 years and whether these could be explained by changes in hydrology or water chemistry. Declines of 53%–100% in the abundance of three migratory fish species were detected in the Muskeg watershed (15% land change). Significant changes in fish health were detected. The largest decreases in body condition of fish in the region occurred in the late 1990s and coincided with elevated levels of fin erosion, the most frequently occurring external abnormality, and with extreme discharge conditions. Fish habitat can be affected by both increases and decreases in discharge, and the most pronounced changes were increases in some watersheds of up to 20% of average discharge post-development. In contrast, decreases in discharge post-development in the Muskeg and Steepbank rivers correlated with a decrease in precipitation. Our results show that climatic events and landscape features such as wetlands are important for understanding changes in the system. Further research is needed to examine potential ecological consequences of the observed changes in hydrology for fish and to explore what caused the changes in migratory fish communities and fish health. This will require a better understanding of the trophic structure of the system and a better monitoring program for migratory fish.