Marine sediment may contain both settled phytoplankton and benthic microalgae (BMA). In river-dominated, shallow continental shelf systems, spatial, and temporal heterogeneity in sediment type and water-column characteristics (e.g., turbidity and primary productivity) may promote spatial variation in the relative contribution of these two sources to the sediment organic matter pool available to benthic consumers. Here we use photosynthetic pigment analysis and microscopic examination of sediment microalgae to investigate how the biomass, composition, and degradation state of sediment-associated microalgae vary along the Louisiana (USA) inner shelf, a region strongly influenced by the Mississippi River. Three sandy shoals and surrounding muddy sediments with depths ranging from 4 to 20 m were sampled in April, August, and October 2007. Pigment composition suggested that sediment microalgae were primarily diatoms at all locations. We found no significant differences in sediment chlorophyll a concentrations (8–77 mg m −2) at the shoal and off-shoal stations. Epipelic pennate diatoms (considered indicative of BMA) made up a significantly greater proportion of sediment diatoms at sandy (50–98%) compared to more silty off-shoal stations (16–56%). The percentage of centric diatoms (indicators of settled phytoplankton) in the sediment was highest in August. Sediment total pheopigment concentrations on sandy stations (<20 mg m −2) were significantly lower than concentrations at nearby muddy stations (>40 mg m −2), suggesting differences in sediment microalgal degradation state. These observations suggest that BMA predominate in shallow sandy sediments and that phytodetritus predominates at muddy stations. Our results also suggest that the relative proportion of phytodetritus in the benthos was highest where phytoplankton biomass in the overlying water was greatest, independent of sediment type. The high biomass of BMA found on shoals suggests that benthic primary production on sandy sediments represents a potentially significant local source of sediment microalgal carbon that may be utilized by benthic consumers in continental shelf food webs.