The degradation of waterways, including the disruption of natural flow regimes, has led to changes in the distribution and composition of aquatic plant communities of many rivers worldwide. The ecology and status of aquatic plants are less well-understood than other groups of riverine plants, but this knowledge is critical for effective waterway ecosystem management. We investigated spatial variability in the occurrence, richness and extent of aquatic plants across 44 sites in seven major lowland flow-regulated river systems in Victoria, Australia, and tested whether these patterns could be predicted by key flow (discharge, the frequency of high flow events and the number of zero flow days) and non-flow variables (livestock grazing, turbidity and riparian canopy shading). Many sites had either one (25% of sites) or zero (18%) species of aquatic plants present, and assemblages across all systems were dominated by just two species: Cycnogeton procerum and Vallisneria australis. Species richness and extent were highly variable across sites and river systems, but were generally higher at sites with low turbidity, and lower at sites with high mean annual flow or large numbers of zero flow days. As such, sites with low to moderate flow and low turbidity will have the greatest potential to support aquatic plant communities. Environmental flows are likely to be most effective in enhancing aquatic plant communities where they can improve water quality, and/or in drier systems where they can be used to reduce the duration of no flow periods.