Bay scallops once supported a vibrant fishery on Long Island. Populations crashed in the mid 1980s due to a series of brown tides, and while blooms haven't occurred within the Peconic Estuary since 1995, scallops have not naturally recovered. Concomitant with the loss of scallops due to the blooms was the disappearance of eelgrass, often called the "preferred" scallop habitat, possibly explaining the lack of recovery. Current restoration efforts have produced over 6 million scallops for deployment to the estuaries, leading to significant increases in the local scallop population. However, it is possible that the loss of seagrass might limit full recovery; this research aimed to investigate the impacts of eelgrass patchiness and alternative habitats on scallop recruitment, survival, and growth. A common theme in marine landscape studies are edge effects, and seagrass edges can affect settlement, access to food, and survival of bay scallops, Argopecten irradians. Using artificial seagrass units, the settlement, recruitment, and survival of bay scallops was investigated across a variety of seagrass patch treatments. By simultaneously collecting settlers (those viable larvae available to settle and metamorphose) and recruits (those settlers which survive some period of time, in this case, 6 weeks) on the same collectors, we were able to demonstrate a balance between positive and negative edge effects, resulting in a net neutral effect. Another important aspect to be considered across a seascape is potential trade-offs between growth and survival. Despite different growth rates across the three years studied, the pattern in growth and condition remained the same - highest in unvegetated sediments, intermediate at patch edges and slowest in patch interiors, which suggests a biological cost for scallops associated with seagrass habitats. Survival of tethered scallops showed an opposite pattern, however, being highest in patch interiors and lowest over barren sediment, and thus showed a potential food-risk trade-off for the scallops in seagrass patches. Further, by examining the core area index (CAI), the data suggest that growth and survival intercept at a low CAI, suggesting that smaller and/or more complex shaped patches may maximize growth and survival. While eelgrass is generally regarded as the preferred habitat of bay scallops, it is disappearing throughout its range, so alternative substrates may serve important ecological functions for bay scallops. One candidate is Codium fragile, a introduced macroalgal species with which bay scallops are known to associate in Long Island, New York. By using both free-released and tethered scallops for a period of 7 days within eelgrass and Codium habitats, this research demonstrated that the invader offers the same predation refuge value. Additionally, densities of naturally recruited 0+ yr scallops recovered by visual and suction dredge sampling were similar in the eelgrass and Codium substrates. This work suggests that Codium might be a viable alternative habitat for scallops. However, since scallops exhibit a food-risk trade-off in their preferred habitat, the complex canopy can have impacts on scallop growth. Growth of scallops placed in Codium was compared to eelgrass and unvegetated sediments by placing caged scallops within each of 3 habitats at 2 hydrodynamically different sites over 2 years. Scallops were measured for long term (3 month) survival, growth, and condition. In 3 of the 4 experiments, scallops exhibited no negative effects of Codium association. In the only experiment where scallops in Codium were negatively affected, the results differed from natural scallops in invaded habitat. This reiterates that Codium may be a viable replacement habitat for bay scallops, although it highlights the complex relationships between invasive engineers and native species. The general conclusions from this study suggest two major shifts from current paradigms in marine ecological literature. First, fragmented seagrass meadows may be beneficial for populations of associated fauna, such as bay scallops. Enhanced settlement and growth at edges, and similar densities of scallops across a seagrass landscape suggests that scallop population growth is reliant on these edge habitats. Second, invasive species may facilitate native species. In the absence of seagrass, this research has demonstrated that an invasive macroalgae may facilitate typically seagrass-associating fauna. Scallop survival is the same in Codium with no additional metabolic costs. These results, in sum, provide valuable information for management and restoration efforts.