Zooplankton species composition, dominant species, and average biomass and abundance were compared between samples taken in the Minjiang River and Jiaojiang River estuaries in September 2008 and August 2010, respectively. The contribution of the dominant species to the total abundance was also determined. Diffe- rences in the zooplankton of the two estuaries were evaluated with respect to each estuary’s water mass properties, and the bait characteristics and value of the fishery of the two areas were also compared. The results indicated that the zooplankton species composition of the Jiaojiang estuary fishing grounds was of higher quality than that of the Minjiang estuary. The Jiaojiang estuary had larger Copepodaand also contained the genera Mysidacea, Pteropoda, and Amphipoda, which the Minjiang estuary lacked. Strong summertime upwelling and run-off created nutrient-rich conditions in the Jiaojiang estuary that supported large zooplankton communities with an average abundance of 281.17 ind. The warm temperate species was most dominant, averaging 121.19 ind.The waters of the Minjiang estuary were lower in nutrients because the estuary was influenced by the nutrient-poor Taiwan Warm Current in summer. Average zooplankton abundance in the Minjiang estuary was 110.19indEvadneter gestina, the most dominant species, averaging 45.63ind.The Jiaojiang estuary surpassed the Minjiang estuary in species composition, zooplankton abundance, and overall quality of its fishing grounds. Comparison between the quantitative characteristics of the zooplankton and water masses of the Minjiang and Jiaojiang estuaries indicated general differences between the fishing grounds and larger migrant fish populations in the Jiaojiang estuary.