The Florida bay scallop (Argopecten irradians concentricus Say, 1822) is a relatively short-lived species that resides in dynamic marine systems and is subject to multiple stressors, although the environmental drivers of bay scallop abundance along the Florida Gulf Coast are not well understood. The use of an ecosystem approach to fisheries management may be particularly relevant for short-lived species that are highly susceptible to environmental changes, but this approach requires an understanding of how environmental variables, such as salinity and temperature, may influence bay scallops throughout their range. This study was designed to identify the relationships between environmental variables and bay scallop abundance and to evaluate the relative effect of these relationships. Scallop surveys conducted in the spring and fall along the Florida Gulf Coast from 1992 to 2019 were compared with seasonal water quality parameters, streamflow discharge, precipitation, wind speed, and climate indices. The size and spawning success of the fall scallop population were negatively affected by relatively high Karenia brevis counts, low dissolved oxygen, and low phosphorus availability. During the period of early postsettlement growth in the winter, scallops were negatively impacted by salinities outside the range of 22–27 due to increased rainfall and low nitrogen availability. Finally, the factors that negatively affected juvenile scallop growth and survival in the spring included increased rainfall and wind speed resulting in relatively high turbidity and comparatively low chlorophyll a.