Estuaries and lagoons are recognized as some of the nursery habitat for the coastal ecosystem and providing essential ecosystem services to human societies while also facing significant threats from human activities and climate change. However, long-term monitoring data for these types of ecosystems remain scarce. This dataset presents the occurrences and morphological measurements of fish collected from the Qigu Lagoon over seven years (2015–2021). Additionally, it includes the physicochemical parameters of the water over four years (2018–2021). A total of 15,009 individual fish representing 190 species were collected. The Leiognathidae, Clupeidae and Mugilidae were the dominant families while the Eubleekeria splendens, Leiognathus equulus, Planiliza macrolepis, Nematalosa japonica and Nuchequula mannusella were the dominant species. This dataset can be regarded as the baseline to help understanding the interannual changes in the fish assemblages accompanied with environmental change. It may provide valuable references for researchers in related fields and managers of estuaries and coastal lagoons.