Riverine systems are important sites for the production, transport, and transformation of organic matter. Much of the organic matter processing is carried out by heterotrophic microbial communities, whose activities may be spatially and temporally variable. In an effort to capture and evaluate some of this variability, we sampled four sites-two upstream and two downstream-at each of two North Carolina rivers (the Neuse River and the Tar-Pamlico River) ca. twelve times over a time period of 20 months from 2010 to 2012. At all of the sites and dates, we measured the activities of extracellular enzymes used to hydrolyze polysaccharides and peptides, and thus to initiate heterotrophic carbon processing. We additionally measured bacterial abundance, bacterial production, phosphatase activities, and dissolved organic carbon (DOC) concentrations. Concurrent collection of physical data (stream flow, temperature, salinity, dissolved oxygen) enabled us to explore possible connections between physiochemical parameters and microbial activities throughout this time period. The two rivers, both of which drain into Pamlico Sound, differed somewhat in microbial activities and characteristics: the Tar-Pamlico River showed higher β-glucosidase and phosphatase activities, and frequently had higher peptidase activities at the lower reaches, than the Neuse River. The lower reaches of the Neuse River, however, had much higher DOC concentrations than any site in the Tar River. Both rivers showed activities of a broad range of polysaccharide hydrolases through all stations and seasons, suggesting that the microbial communities are well-equipped to access enzymatically a broad range of substrates. Considerable temporal and spatial variability in microbial activities was evident, variability that was not closely related to factors such as temperature and season. However, Hurricane Irene's passage through North Carolina coincided with higher concentrations of DOC at the downstream sampling sites of both rivers. This DOC maximum persisted into the month following the hurricane, when it continued to stimulate bacterial protein production and phosphatase activity in the Neuse River, but not in the Tar-Pamlico River. Microbial community activities are related to a complex array of factors, whose interactions vary considerably with time and space.