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More frequent extreme climate events (e.g., extreme precipitation) are to be expected in the future, and such events may potentially have significant effects on freshwater ecosystems. In the present mesocosm study, the effects of simulated extreme precipitation on submerged macrophytes were evaluated for three different macrophyte community (MC) treatments (MC1, MC2 and MC3). MC1 consisted of only Vallisneria denseserrulata, while MC2 and MC3 included three and six species of various growth forms. Two treatments of extreme precipitation (EP) were simulated-an extreme treatment (E) simulating a sudden increase of water level from 75 cm to 150 cm within one day and a gradual treatment (G) simulating an increase to the same water level within 3 months, combined with two control treatments. Total macrophyte community biomass was resilient to the EP and MC treatments, while species-specific variations in responses, in terms of biomass, maximum height, and sexual reproduction, were found. For instance, E led to earlier flowering of Potamogeton lucens and production of more flowers, while it had adverse effects on the flowering of Ottelia alismoides. We conclude that freshwater ecosystems with high coverage of submerged macrophytes may be overall resilient to extreme precipitation under nutrient-limited conditions, especially communities with diverse growth forms.