Surveying the abundance, demography and behaviors of marine fishes is a difficult task due to the challenge of collecting observations in environments that are difficult for researchers to access. Moreover, these challenges are often magnified when attempting to study fishes that are rare, threatened or endangered. In many instances, such species have become rare because they aggregate to reproduce at known times and places, and, are thus, susceptible to harvest during reproduction. Here, I focus on three species in two different environments: Steelhead (Oncorhynchus mykiss) returning to streams to spawn in Washington, and spawning aggregations of Nassau Grouper (Epinephelus striatus) and Tiger Grouper (Mycteroperca tigris) in the Cayman Islands. By taking advantage of the reproductive aggregations of these species, I can generate observations of behavior and life-history to inform effective management. For Steelhead, I developed a new hierarchical nested Bayesian patch occupancy model that estimates movement rates throughout a river network based on the observed movements of PIT (passive integrated transponder) tagged fish from a network of in-stream tag detectors. Using these movement rates and estimates of dam passage below the in-stream detectors, I was able to, for the first time, generate estimates of abundance of this threatened species throughout the river network. For Nassau Grouper, I developed an integrated population model that incorporated both video observations and tagging data to obtain a fourteen-year time series of abundance in the Cayman Islands. Based on these modeling efforts, I demonstrated that management efforts have resulted in a dramatic recovery of this endangered fish in the Cayman Islands. Finally, using eggs collected from spawning aggregations of Nassau Grouper and Tiger Grouper, I documented fertilization rates and the variable morphology of eggs between spawning events. Using laboratory studies, I demonstrated that warming water temperatures are likely to decrease larval survival for Nassau Grouper, although the impact was variable, suggesting there may be adaptive capacity within the population to respond to impending warming. Across each of these studies, I leveraged reproductive aggregation, a perceived vulnerability in the life history of fishes, to generate observations and synthesis in support of fisheries restoration and conservation.