Lake Kasumigaura is the second largest lake in Japan. A long-term monitoring program has been conducted by National Institute for Environmental Studies, Japan. Fish and shrimp samples were monitored in cooperation with a local professional fisherman every 2 to 3 months since 2005. This data set includes 46 fish species, 3 shrimp species and 1 frog species. These data are fishery-independent time-series data.