The present study was designed to investigate the seasonal changes in the abundance and biomass of zooplankton and their relationships with water quality parameters in mudflat shallow estuary, Helleh River, Persian Gulf (Iran). The zooplankton consisted of Acartia sp., Euterpina sp., Oithona spp., Oncaea sp., Paracalanus sp., Corycaeus sp., Labidocera sp., Macrosetella sp., Microsetella sp., Temora sp., copepod copepodid, copepod nauplii, Barnacle, Polychaeta, Conchoecia sp. (Ostracoda), Hyperid, Decapoda (zoea and megalopa), Actinula, Echinopluteus, Mollusca, Tintinnopsis sp., Ctenophora (Boliopsis sp.), Protozoa (Discorbis sp.), cumacea (Diastylis sp.), Cnidaria (Siphonophora and Phialidium), Nematoda (Pratylenchus spp.), Urocordata (Oikopleura spp.), fish eggs and fish larvae. The maximum biomass was estimated at estuary mouth in all seasons, the highest values in autumn (97.8-255.6 mg/m³) and the lowest in winter (5.5-68.2 mg/m³). The seasonal abundance (density) of zooplankton was 21237±2419, 45739±6053, 5242±648, and 12905±1867 ind./m³ in summer, autumn, winter and spring, respectively. There was a significant correlation (P<0.01) between zooplankton abundance as well as biomass with salinity, dissolved oxygen and chlorophyll a. Based on PCA (Principal Component Analysis), the most important factors in mudflat shallow river–estuarine system that could describe most changes of biomass and abundance of zooplankton were salinity, chlorophyll a, temperature and pH,  respectively.