A seven-year monitoring on fish community around the Qigu Lagoon located on the southwest coast of Taiwan.

Estuaries and lagoons are recognized as vital nursery habitats for coastal ecosystems, 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 ecosystems remain scarce. This dataset presents the occurrences and morphological measurements of fish collected from the Qigu Lagoon over a seven-year period (2015-2021). Additionally, seven water quality parameters which are basic to aquatic life over four years (2018-2021) are included. A total of 15,009 individuals representing 190 species were collected. Among the families, Leiognathidae, Clupeidae, and Mugilidae were the most abundant, while the dominant species included Eubleekeria splendens, Leiognathus equulus, Planiliza macrolepis, Nematalosa japonica, and Nuchequula mannusella. This dataset serves as a baseline for understanding interannual changes in fish assemblages in relation to environmental changes. It may provide valuable references for researchers in related fields and for managers of estuaries and coastal lagoons.