We investigated whether environmental filtering or dispersal-related factors mostly drive helophyte and hydrophyte species richness and community composition in 93 lakes situated in Baikal Siberia. Using partial linear regression and partial redundancy analysis, we studied (1) what are the relative roles of environmental variables, dispersal variables, spatial processes and region identity (i.e., river basins) in explaining variation in the species richness and species composition of helophytes and hydrophytes across 93 Siberian lakes, and (2) what are the differences in the most important explanatory variables driving community variation in helophytes versus hydrophytes? We found that, for both species richness and species composition, environmental variables clearly explained most variation for both plant groups, followed by region identity and dispersal-related variables. Spatial variables were significant only for the species composition of hydrophytes. Nutrient-salinity index, a proxy for habitat trophic-salinity status, was by far the most significant environmental determinant of helophytes and hydrophytes. Our results indicate that environmental factors explained the most variation in both species richness and species composition of helophytes and hydrophytes. Nevertheless, dispersal-related variables (i.e. spatial and dispersal) were also influential but less important than environmental factors. Furthermore, the dispersal-related variables were more important for hydrophytes than for helophytes. Most brackish permanent lakes were mostly located in the steppe biomes of southern Transbaikalia. This characteristic along with the oldest age, the largest distances to both river and settlements and the lowest temperatures in the study region distinguished them from freshwater, drained and more nutrient-rich floodplain lakes.