Wetlands in the floodplains of flood-control impoundments are exposed to different hydrologic conditions than those in natural systems. To gain insight into the impact of hydrology on wetland communities, we examined associations between crustacean zooplankton community structure and hydrologic and local environmental characteristics in 29 ponds surrounding a flood-control reservoir. Fifty-eight species of zooplankton were detected among all ponds, and local species richness ranged from 3–16. Depth and distance from the lake were the most important predictors of species richness and provided 31% of the explanation for variation among ponds. Non-metric multidimensional scaling (NMDS) provided visualization of factors important to community structure. Analysis of similarities revealed hydroperiod and flood frequency were significant factors structuring communities. These results suggest that hydrology has a significant effect on both species richness and community structure of zooplankton communities in floodplain ponds. Elucidating the importance of hydrology to wetlands residing in managed floodplains should assist reservoir managers in understanding the impacts of different management regimes on regional ecology.