Aquatic bacteria respond to changing environmental conditions through a variety of mechanisms including changes in abundance, shifts in community composition and variable activity states. In the tidal-freshwater James River, variation in bacterial abundance was linked to nutrient availability and autochthonous production with highest bacterial densities associated with low-nutrient, high-chlorophyll a conditions. Laboratory experiments revealed that bacterial growth rates were nutrient limited at the low-nutrient site, while co-limitation (nutrients, glucose, light) was apparent at the high nutrient site. Despite large differences in abundance, community composition was similar based on TRFLP and 16S rDNA pyrosequencing. Community similarity was lower among rRNA libraries suggesting that variable activity states are prevalent in natural communities. Rare taxa were more likely to be metabolically active and were capable of dramatic growth under microcosm conditions.