Wanshan Archipelago plays an important role in the conservation of fishery resources in the Pearl River Estuary. However, there is still a lack of sufficient research on the fishery ecological status of the adjacent waters of islands and reefs in this region. Thus, we analyzed the characteristics of the seawater environment and zooplankton community in Wanshan Archipelago in April 2021. The results show that the seawater environment of Wanshan Archipelago was greatly influenced by fresh water input from the Pearl River coastal channels. Consequently, the concentration of dissolved inorganic nitrogen, nutrient quality index and eutrophication index were higher in the adjacent sea areas of Guishan Island and Dong'ao Island which are located in the northwestern Wanshan Archipelago. Eutrophication was observed in this area. Furthermore, the primary production in the seawater of these two islands was also higher, most with medium and low levels. The zooplankton communities of Wanshan Archipelago can be divided into three groups, and one of them affiliated to the adjacent sea areas of Guishan Island had a low Shannon-Wiener index value, indicating a potentially polluted seawater environment. However, high abundances of spawning and larval fish were observed at Guishan Island (133 egg·m−3
and 18 ind·m−3
, respectively), suggesting that it is an important fish spawning area. The primary production and Pielou evenness index of zooplankton can reflect the correlation between water environment and zooplankton community in Wanshan Archipelago, and can indicate the state of water eutrophication.