Submersed aquatic plants have a key role in maintaining functioning aquatic ecosystems through their effects on the hydrological regime, sedimentation, nutrient cycling and habitat of associated fauna. Modifications of aquatic plant communities, for example through the introduction of invasive species, can alter these functions. In the Sacramento-San Joaquin River Delta, California, a major invasive submersed plant, Brazilian waterweed Egeria densa, has become widespread and greatly affected the functionality of the submersed aquatic plant community. Rapid assessments of the distribution and abundance of this species are therefore crucial to direct management actions early in the season. Given the E. densa bimodal growth pattern (late spring and fall growth peaks), summer assessments of this species may indicate which and where other submersed species may occur and fall assessments may indicate where this and other species may occur in the following spring, primarily because the Delta's winter water temperatures are usually insufficient to kill submersed aquatic plant species. We assessed community composition and distribution in the fall of 2007 and summer of 2008 using geostatistical analysis; and measured summer biomass, temperature, pH, salinity, and turbidity. In the fall of 2007, submersed aquatic plants covered a much higher proportion of the waterways (60.7%) than in the summer of 2008 (37.4%), with a significant overlap between the seasonal distribution of native and nonnative species. Most patches were monospecific, and multispecies patches had significantly higher dominance by E. densa, co-occurring especially with Ceratophyllum demersum. As species richness of non-natives increased there was a significant decrease in richness of natives, and of native biomass. Sustained E. densa summer biomass negatively affected the likelihood of presence of Myriophyllum spicatum, Potamogeton crispus, and Elodea canadensis but not their biomass within patches. Depth, temperature and salinity were associated with biomass; however, the direction of the effect was species specific. Our results suggest that despite native and invasive non-native submersed plant species sharing available niches in the Delta, E. densa affects aquatic plant community structure and composition by facilitating persistence of some species and reducing the likelihood of establishment of other species. Successful management of this species may therefore facilitate shifts in existing non-native or native plant species.