Climate change is increasing the frequency, intensity, and unpredictability of extreme events experienced by freshwater communities. These impacts, which include unseasonal floods and droughts, can disrupt historically predictable hydroperiod patterns. Therefore, understanding how communities with differing natural disturbance histories respond to hydrological stochasticity is critical for predicting future pond resilience under ecosystem change. We explored shifts in pond community structure challenged with altered hydroperiod regimes using frameworks of species diversity (richness) and phenotypic flexibility (body size variability). Communities that experience regular disturbances, such as seasonal pond drying, are expected to support populations with flexible life-history strategies and higher body size variability, whereas communities from perennial ponds may exhibit higher species diversity but lower flexibility in body size response. Thus, we tested whether communities emerging under stochastic hydroperiod conditions are characterized primarily by species diversity, trait flexibility, or a combination of both, and whether these mechanisms differ among communities with contrasting disturbance histories. We conducted a fully factorial mesocosm experiment using two community types—sourced from ephemeral and perennial ponds—and three hydroperiod regimes—stable, drying, and stochastic. We used stovepipe samples to stock mesocosms with zooplankton, macroinvertebrates, amphibian, and fish species in naturally relevant densities from these two pond types. We observed pronounced differences in community composition, body size structure, and developmental patterns across hydroperiod treatments, and particularly under stochastic drying regimes. Community responses varied depending on disturbance history, with taxa exhibiting differential responses in species and body size diversity. These patterns suggest that increasing hydroperiod variability can restructure freshwater communities through multiple, potentially interacting mechanisms with implications for predicting community organization under future climate scenarios.