Benthic microalgae (BMA) are an abundant and common component of the illuminated surface sediments of shallow continental shelves worldwide. Although phytoplankton biomass, community composition, and productivity are relatively well documented for these habitats, little is known about the community dynamics of BMA in these systems. We determined the community composition and seasonal abundance of BMA in the surface sediments of shallow (ca. 10–13 m) nearshore shelf waters off Charleston, SC. Our primary hypothesis was that BMA exhibit seasonality in abundance and, similarly, abundance is correlated with bottom water temperatures. BMA had a high spatial variability (CV = 20–50%) over m to km scales. BMA biomass in the upper 1 cm of sediments exceeded phytoplankton by a factor of 3 and was composed primarily of diatoms with cyanobacteria and green microalgae (chlorophytes & euglenophytes) as common, but relatively minor components. The BMA community exhibited a seasonal variation in abundance that was positively correlated with bottom water temperature. The highest abundances occurred in the summer months, peaking in August. This study is the first to report the monthly to annual spatiotemporal dynamics of BMA in the nearshore shelf waters of the South Atlantic Bight and offers insights in the potential contribution of BMA to shelf primary productivity.