Shallow lakes and ponds are often characterised either by clear water with abundant submerged macrophytes or by turbid water with abundant phytoplankton. Blooms of toxic filamentous blue-green algae (cyanobacteria) often dominate the phytoplankton community in eutrophic lakes, which threatens ecological functions and biodiversity of freshwater ecosystems. We studied a simple lake model in order to evaluate individual and combined suppressive effects of rooted submerged and rooted floating-leaved macrophytes on algal blooms. Floating-leaved plants are superior competitors for light, whereas submerged plants absorb and reduce available phosphorus in a water column that rooted floating-leaved plants exploit to a lesser extent. We found that mixed vegetation that includes both submerged and floating-leaved plants is more resistant than vegetation comprised by a single plant type to algal invasion triggered by phosphorus loading. In addition, competitive exclusion of submerged plants by floating-leaved plants may promote an algal bloom. These predictions were confirmed by the decision tree analysis of field data from 35 irrigation ponds in Hyogo Prefecture, Japan.