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Hydrological characteristics of freshwater ecosystems are powerful determinants of the distribution of biological communities and changes in environmental factors. This study identified relationships between the wetland environment, rotifer community, and hydrological factors for 48 wetlands, to determine their impact on wetland conservation and management. Different hydrological factors produced different wetland environments, which influenced the rotifer community composition. The wetlands with “poor” “in/outflow function” and “shore stability” levels showed high conductivity, turbidity, depth, and concentrations of total nitrogen, total phosphorus, and chlorophyll <i>a</i>. In contrast, the dissolved oxygen levels and velocity were the highest in wetlands with “good” in/outflow function and shore stability variables. The nutritional status of each wetland affected the composition of the rotifer community. Some genera (<i>Keratella</i>, <i>Brachionus</i>, <i>Anuraeopsis</i>, <i>Trichocerca</i>, and <i>Philodina</i>) were found in wetlands with high concentrations of total nitrogen, total phosphorus, and chlorophyll <i>a</i>, and high turbidity and depth. In contrast<i>, Ascomorpha</i> and <i>Ploesoma</i> were found in wetlands with high dissolved oxygen levels and flow velocity. High densities of <i>Lepadella</i>, <i>Lecane,</i> and <i>Testudinella</i> were found in wetlands completely covered by macrophytes. The rotifer community distribution can be used to understand the trophic, current functional, and environmental status of wetlands.