Opportunities for growth and survival of aquatic organisms are spatially and temporally variable as habitat conditions across watersheds respond to interacting climatic, geomorphic, and hydrologic conditions. As conservation efforts often focus on identifying and protecting critical habitats, it is important to understand how this spatial and temporal variation in habitat quality affects the production dynamics of populations. Here, we use microchemical records preserved in otoliths to reconstruct juvenile habitat‐use by sockeye salmon that survived to spawn in a single population on the Alaska Peninsula. Successful individuals demonstrated a diverse array of juvenile behavioral strategies both within and among years. Importantly, the dominant juvenile behavioral strategy used by successful individuals changed among years, suggesting shifts in the relative benefits of different rearing habitats. The growth benefits of remaining in a more productive rearing lake were greatest in warm years indicating environmental influence on relative habitat quality. However, we found no strong relationship between the amount of growth accumulated in the productive rearing lake and overall population productivity across years. These results highlight the dynamic nature of habitat conditions and the beneficial effect of maintaining connectivity between diverse habitats for population productivity. When short‐term studies are used to demonstrate the relative values of different habitats to species of conservation concern, there is a distinct risk of under‐valuing habitats that may be critically important under alternative environmental conditions. In particular, land‐use decisions that reduce the range of habitat options available to species may erode a population’s ability to withstand environmental change over the long term.