ABSTRACT: Spatial and temporal variability characterize submerged aquatic vegetation (SAV) assemblages, but understanding the complex interactions of environmental drivers of SAV assemblages remains elusive. We documented SAV composition and biomass across a salinity gradient in a coastal estuary over 12 mo. Ten macrophyte species were identified. The dominant species, Ceratophyllum demersum and Myriophyllum spicatum, accounted for over 40% of total biomass. Only Ruppia maritima occurred across the salinity gradient. Salinity, water depth and clarity delineated 3 assemblages: a saline assemblage, and 2 groups of fresher-water species, one associated with deeper water and lower water clarity and the other associated with shallow water and higher water clarity. These assemblages exhibited intra-annual variation, with at least 5 times more biomass in late spring/mid-summer compared to early winter. This pattern was consistent across the estuary, although the difference between peak and low biomass varied by habitat type; brackish exhibited the greatest magnitude. This variation is likely due to higher variation in salinity and the species composition of this habitat. As climate change and coastal restoration impact timing and range of salinity, water depth and clarity in this region, these data can be used to help inform predictive models and management decisions.