Data set presents results from fish biometry field work within four lakes in Japan (Suzuuchi, Funazawa, Kashiramori, Abakuma). Data comprise sampling location, fish species, sex, length, weight (total fish, gonad and liver weight). Fish were sampled during May 2017; target species included crucian carp, common carp and smallmouth bass. For the health and reproductive status assessment, fish of similar weight and total length were collected. Gill nets (20 m length and 21 mm mesh size) were employed to ensure capture of homogeneous groups of mature fish. The work described here was conducted under the TREE project (http://tree.ceh.ac.uk/) funded by the Natural Environment Research Council, Environment Agency and Radioactive Waste Management Ltd. Full details about this dataset can be found at https://doi.org/10.5285/07347484-5d35-4335-bdbe-ac9d7b33c84f