Marine bacterial communities show strong spatial and seasonal patterns, often characterized by changes at high taxonomic levels. The Pelagibacteraceae are common members of bacterial communities, with well-documented biogeography at the subclade level. To identify patterns within the subclades, the abundance and diversity of Pelagibacteraceae were analyzed over a two-year period at four stations across an estuarine gradient. Pelagibacteraceae was the most abundant bacterial family, averaging 27% of the community, but varying from 1% to 57% in any one sample. Highest abundances were detected in autumn and winter. Pelagibacteraceae richness was lowest at the most inshore site, and highest in autumn and winter at all sites. Shannon diversity decreased in winter, when a few OTUs dominated the community. Dissolved oxygen, dissolved silicate and prokaryote abundance explained most of the variability in the Pelagibacteraceae communities, with salinity differentiating low salinity communities. The 10 most abundant OTUs included OTUs that varied across sites, with little seasonality as well as those with small site effects, but strong seasonal patterns indicating differences in the niches of individual OTUs. While salinity was important in structuring low salinity communities, higher salinity communities appear to be responding to additional environmental parameters including oxygen, nutrients and other organisms.