In response to the degradation of coastal environments and their associated habitats, managers and policy makers have looked to utilize population dynamics and, more specifically, connectivity (i.e., import and export of larvae, juveniles, and adults) in order to rebuild stocks. As the majority of population bottlenecks are thought to result from critical periods experienced in earlier life stages, it is particularly important to discern movement patters during larval and juvenile stages. This study used two estuarine-associated model organisms, the Eastern oyster and the black sea bass, to examine connectivity at the larval and juvenile stages, respectively. A requisite to tracking larval dispersal of the Eastern oyster was to explore the utility of geochemical tagging methods within our study system, the Pamlico Sound. Strong environmental (e.g., temperature and salinity) gradients were present over regional (~ 35 x 15 km quadrants) scales and both larval and settler shells were able to generate distinct, multi-elemental signatures between putative natal and settlement sites. These methods were then applied, with a combination of larval outplanting techniques (i.e., stationary moorings and floating surface drifters), to show that larval dispersal is single-source driven, generally follows wind-driven currents, and leads to high amounts of self-recruitment. However, dispersal pathways are not uniform across the Sound and seasonal and annual dispersal patterns can be highly variable. Geochemical tagging of black sea bass showed that estuarine nurseries, such as oyster reefs, contribute over 89% of the juvenile black sea bass to the adult stock; however, there is significant annual variation in contribution. The role of estuarine habitats becomes even more complex for the protogynous black sea bass, as fish exhibited carry-over effects (COEs) related to nursery habitats: juveniles that utilized estuarine nurseries transitioned from female to male six months earlier than juveniles that utilized offshore nurseries. This dissertation provides substantial support for the implementation of habitat-based management plans rather than single-species management practices, which cannot account for seasonal and annual variation inherent in dispersal pathways or variable reproductive (and dispersal) potential among subpopulations.