Knowledge of changes in the interdependence of a species' populations for continued existence (connectivity) and of the forces driving connectivity patterns is critical for management and conservation of the species. Population genetics can be used to investigate population connectivity. Combining population genetics with climatic, environmental, and biological (external) factors that can influence population structure and connectivity can lead to a greater understanding of the forces influencing population dynamics. We deciphered the population genetic structure and connectivity patterns of bay scallops (Argopecten irradians concentricus Lamarck) from Florida Gulf of Mexico waters using allozyme-locus and mitochondrial DNA population genetics data from samples representing four consecutive generations. We evaluated bay scallop population genetic relationships within the context of habitat, hydrodynamic, and environmental variation, and concomitant spatial patterns in the abundance of adult and recently recruited scallops to infer the influence of these factors on bay scallop population structure. Florida Gulf bay scallops form a hierarchical, mixed-model, source-sink metapopulation with intergenerational variation in connectivity that seems to be influenced by the factors we considered. An El Niño event that occurred during 1 y caused climatic and environmental change that greatly reduced subpopulation connectivity, allowing us to understand more completely the potential relative importance of the other external factors on change in metapopulation connectivity over time. Our study illustrates the value of using multiple genetic markers, sampling for multiple years, and integrating data from multiple external factors for understanding the population genetic structure of species for adaptive management.