Invasive species continue to have a pervasive influence on biodiversity but it is often unclear how invasive species affect native species. In field observations and greenhouse experiments, I examined the effect of the non-native submersed aquatic plant Hydrilla verticillata on the native species Vallisneria americana. Field monitoring from 2002 to 2006 showed that coverage of species peaked in 2004 after initial invasion of the estuarine study system in 2002. Substrate characteristics did not limit species distribution. In contrast, substrate and planting density affected plant growth and the outcome of intra- and inter-specific competition in the greenhouse. Although other environmental variables, such as water depth and turbidity, appear to override the effect of substrate in the field, the greenhouse experiment suggests that substrate can be an important driver of submersed aquatic plant community dynamics. Sediment characteristics should therefore be a factor in restoration design and the management of invasive species.