Understanding the mechanisms by which populations are regulated is critical for predicting the effects of large-scale perturbations. While discrete mortality events provide clear evidence of direct impacts, indirect pathways are more difficult to assess but may play important roles in population and ecosystem dynamics. Here, we use multi-state occupancy models to analyze a long-term dataset on nesting bald eagles in south-central Alaska with the goal of identifying both direct and indirect mechanisms influencing reproductive output in this apex predator. We found that the probabilities of both nest occupancy and success were higher in the portion of the study area where water turbidity was low, supporting the hypothesis that access to aquatic prey is a critical factor limiting the reproductive output of eagles in this system. As expected, nest success was also positively related to salmon abundance; however, the negative effect of spring warmth suggested that access to salmon resources is indirectly diminished in warm springs as a consequence of increased glacial melt. Together, these findings reveal complex interrelationships between a critical prey resource and large-scale weather and climate processes which likely alter the accessibility of resources rather than directly affecting resource abundance. While important for understanding bald eagle reproductive dynamics in this system specifically, our results have broader implications that suggest complex interrelationships among system components.