We examined benthic microbial communities in three contrasting subtidal salt marsh sediments over the course of a year to investigate the relationship between environmental conditions and benthic microbial community structure. Samples were collected monthly from a high energy, sandy beach, a tidal creek bed, and a Spartina alterniflora marsh border. The concentrations and biomasses of benthic microalgae (BMA), total and potentially active bacteria (measured by an enzyme-activated fluorogenic compound), heterotrophic protists, and metazoan meiofauna were measured at each location. Sediment grain size and porewater pH explained most of the variability in biomass distributions; variations in benthic biomass did not correlate well with temperature. There was a seasonal shift from a BMA-dominated community in the spring and summer months to bacteria-dominated communities in the autumn at all locations, when inactive bacteria were most abundant. When normalized to sediment porewater volume, benthic protists concentrations were not significantly related to sediment porosity. Benthic protist porewater concentrations (mean: 3.4x103, range: 0.1–9.3 x 103 protists ml-1) were comparable to protist concentrations in the water column. In contrast, bacteria were several orders of magnitude more concentrated in the sediments (mean: 4.2x109; range: 0.6 – 16x109 bacteria ml-1) than the water column. Low abundances of protists relative to bacteria appear to contribute to long bacterial turnover times, especially in fine grained sediments. We hypothesize that both grazing by meiofauna and low anaerobic growth efficiency lead to relatively low biomass of bacterivorous protists.