Estuaries are dynamic ecosystems, acting as intermediaries between freshwater and marine systems,  nurseries, and critical areas of microbial organic matter transformations. Estuarine microbes vary in space and time; however, little is known about the controls of bacterial abundance and growth. We examined the effects of season, nutrient concentrations, and salinity in shaping bacterial diversity, abundance, function, and growth in two Mid-Atlantic estuaries, the Delaware and Chesapeake Bays. We assembled >300 medium and high-quality metagenome assembled genomes representing over 50% of the bacterial community. The two most abundant classes were Alphaproteobacteria and Acidimicrobiia (Actinobacteria), with 12 and 11 families represented, respectively.  The most dominant family was Pelagibacteraceae with 11 genomospecies, making up to 60% of the community in the spring and 30% in the summer. Variations in abundance and activity were correlated with environmental factors, including season, salinity, size fraction, as well as microbial pathways, including carbohydrate metabolism, lithotrophy, and substrate transport. Variations in growth rate and activity were correlated with species, bay, season, and nutrient concentrations. In general, species abundance correlated with activity, as measured by transcript abundance, but not with growth rate.  Our results underscore the variability in estuarine ecosystems.  Furthermore, abundance, activity and growth rate are not necessarily correlated with each other but can be explained by variations in the estuarine environment.