Nansi Lake and Hongze Lake are both water storage lakes along the East Route of the South-to-North Water Transfer project (ESNT). Frequent changes in hydrologic properties are responsible factors for controlling the zooplankton community assemblages in both lakes, so we studied the possible influence of water transfer and environmental factors on zooplankton community structure and abundance. Zooplankton assemblages were investigated seasonally for one year in both lakes; a total of 133 and 122 zooplankton taxa were identified in Nansi Lake and Hongze Lake, respectively. The most dominant rotifer species were littoral, e.g., Keratella tecta, Keratella valga and Lecane lunaris in Nansi Lake and Brachionus angularis , Brachionus forficula and Polyarthra vulgaris in Hongze Lake. Comparatively, Nansi Lake had a higher Shannon-Wiener diversity index value (5.13), while Hongze Lake had a higher species richness index (4.21). The average number of zooplankton across seasons in Nansi Lake (protozoa: 774±63 ind./L, rotifers: 4 817±212 ind./L, cladocerans: 896±14 ind./L, copepod: 435±42 ind./L) was comparatively lower than Hongze Lake (protozoa: 1 238±63 ind./L, rotifers: 6 576±112 ind./L, cladocerans: 1 013±20 ind./L, copepod: 534±25 ind./L). Canonical correspondence analysis identified differing environmental gradients that were most responsible for influencing zooplankton communities in the two lakes (Hongze Lake: NH 4 -N, total nitrogen, transparency and pH; Nansi: pH, temperature and total phosphorus). Frequent changes related to water transfer in lakes favoured the diversity of rotifers and protozoa communities. Zooplankton habitat preference, changes in community structure and opportunistic peaks and extinction of certain taxa were also observed in the study lakes.