Bacteria dominate in abundance, diversity and potentially metabolic activity in most environments. Our current knowledge on the influence of specific individual taxa on biogeochemical processes involving DOM is largely lacking. We chose to examine a variety of microbial populations in estuaries, because they are a natural habitat of continuous spatial as well as seasonal environmental change. We hypothesize estuarine microbes are greatly influenced by DOM type.   Size fractionated samples were collected from surface water along the salinity gradient of the Delaware Bay during March, August and November of 2014 and in April and August 2015 from the Chesapeake Bay. Both DNA and cDNA were sequenced by JGI from 24 selected samples from low, mid and high salinity sites within the bay. We characterized the abundance, distribution, replication rates and differential gene expression patterns of several metagenome assembled genomes (MAGs), phylogenetically associated with the SAR11 clade, Rhodobacterales order and Bacteroidetes phylum. Overall, the most change in abundance and gene expression of individual populations occurred between seasons and salinities, with lesser amounts of differential replication and gene expression between size fractions.  Time of day had variable numbers of genes differentially expressed, depending on the taxon.  Many genes were differentially expressed in taxa associated with the Rhodobacteriales as well as the SAR11 and Bacteroidetes groups. Additionally, we observed niche specificity in gene content and expression, especially in the SAR11 clade. Our results demonstrate the breadth of both functional potential and functions of individual bacterial populations in estuarine environments. Furthermore, our results indicate that abundance and activity of estuarine microbial populations change due to differences in DOM content, as evidenced by the different nutrient uptake and utilization genes expressed between seasons and salinities.