The area surrounding the Hau River is one of the most important aquaculture and fisheries areas in the Mekong Delta, Vietnam. Fish, shrimp farms and fishers rely of the natural zooplankton production in the incoming water to sustain production. Zooplankton samples were collected from July  2017 to June  2018 using a zooplankton net with mesh size of 60 µm at 3 sites on Hau river at Tran De (river mouth), Dai Ngai (midpoint) and Cai Con (farthest salt intrusion area on Hau river). Qualitative and quantitative samples of zooplankton together with salinity level were determined monthly at each sites. The salinity was found to fluctuate from 0 to 20‰ in the study area. A total of 137 zooplankton species were recorded including 26 species of Protozoa (19%), 47 species of Rotifera (34%), 12 species of Cladocera (9%), 44 species of Copepoda (32%) and 8 other taxon (6%). Copepod and rotifer prevailed with high densities (19.9x10³ ind.m^-3 and 19.7x10³ ind.m^-3, respectively), whereas protozoa and cladocera were less abundant with 6.8x10³ ind.m^-3 and 4.9x10³ ind.m^-3, respectively. When salinity increased to more than 5, protozoa and copepods were more abundant and reached a peak at 20 with 25.0x10³ ind.m^-3 and 53.0x10³ ind.m^-3, respectively. Regression analysis indicated that the density of zooplankton was significantly correlated to salinity variation. Protozoa and copepod were positively correlated with salinity, whereas cladocera and rotifer were negatively correlated with salinity. The impacts of climate change could exacerbate the seasonal fluctuations in salinity and zooplankton composition.