Abstract: From October 2010 to July 2011, an investigation was conducted on the zooplankton communities in reclaimed and natural waters in Nanhui east tidal flat to study the seasonal variations of the zooplankton’s species composition, abundance, biomass, dominant species, and biodiversity, aimed to explore the differences in the zooplankton’s community structure within and outside the reclaimed waters and the relationships of the community structure with several indispensable environmental factors such as water salinity, water temperature, and human activities. A total of 30 zooplankton species were identified, among which, 24 species were in reclaimed waters and dominated by rotifers, and 14 species were in natural waters and dominated by copepods. The average abundance of the zooplankton was obviously higher in reclaimed waters than in natural waters, but the average biomass was in adverse. The dominant species in reclaimed waters were freshwater species, such as Brachionus angularis, Bcalyciflorus, and Mesocyclops leuckarti, while those in natural waters were brackish species, such as Sinocalanus sinensis, Schmackeria poplesia, and Tortanus vermiculus. Both in reclaimed and in natural waters, the dominant species had seasonal alternation. The Shannon index (H) and Pielou evenness index (J) of the zooplankton communities were higher in natural waters, but the Margalef species richness (d) and simplicity index (C) were higher in reclaimed waters. Cluster analysis and MDS evaluation indicated that there was an obvious difference in the community structure of zooplankton between reclaimed and natural waters. Reclamation could be the primary cause for the variations of the zooplankton’s community structure in reclaimed waters, and environmental factors such as water salinity and tidal power also contributed to the variations.