In order to understand the spatiotemporal distribution of zooplankton species composition, abundance and biodiversity in the mudflat wetlands of Hangzhou Bay, 40 samples were conducted at middle to high tide levels in five sampling stations (S1-S3 for discharge area, and S4-S5 for non-discharge area) in April (spring), July (summer), October (autumn), 2010 and January (winter), 2011. A total of 38 species of zooplankton (15 Rotifera, 4 Cladocera, 19 Copepoda) were found. The annual average density (88.89 ind./L) and biomass (0.41 mg/L) of zooplankton in the discharge area were much higher than those, i.e., 4.21 ind./L and 0.10 mg/L, respectively, in the non-discharge area. The dominant species of rotifers and copepods in the discharge area were Brachionus calyciflorus and Sinocalanus dorrii, respectively, and Calanus sinicus dominated copepods in the non-discharge area. Water nutrient concentrations, community density, and biomass of the zooplankton at middle tide level in stations S2-S3 were much higher than those at high tide level. The zooplankton community in the mudflat wetlands, the effects of the freshwater discharge, tidal creek spread, and tidal conditions determined the temporal pattern of the main zooplankton species, and the tidal creek spread and tidal conditions explained differences in composition and structure between the middle and the high tide level.