Abstract: The environmental impact caused by thermal discharge waters of power plants is of global concern since thermal discharge directly affects the environmental situation near power plants. The present study used the vital stain neutral red to identify live and dead zooplankton collected from stations at the intake and the outlet of two nuclear power plants (NPPs). Significantly higher mortalities occurred at the outlet station than at the intake station (p < 0.01) at both NPPs. The mortalities of most zooplankton taxa and all zooplankton assemblages were significantly positive correlated to differences of water temperature (ΔT) at NPP I (p < 0.05), whereas it was not significantly positive correlated with ΔT at NPP II (p > 0.05). The weight of organic matter of zooplankton fragments was higher at the outlet station than at the intake station at both NPPs, indicating the physical damage of zooplankton when passing the cooling system.