The paper presents a comparative study of temporal trends of plutonium (239,240Pu), radiocesium (137Cs), and potassium (40K) in samples of three commercial fish species (Northern pike, Baikal grayling, and Siberian dace) occupying different positions in a trophic net in the Yenisei River (Siberia, Russia). Samples of fish were caught in the Yenisei in 2011–2020 during a period of significant changes in controlled radioactive releases into the river. The study has shown no increase in plutonium content in fish samples within two years after the upsurge in controlled Pu discharge into the river (2018–2020). Average activity concentration of 239,240Pu (mBq∙kg− 1 d.w.) in muscle of grayling, 10.90 ± 8.61, was higher (p < 0.01) than in muscle of dace, 2.36 ± 1.25, and pike, 3.75 ± 2.88. This can be attributed to the feeding of grayling on benthic invertebrates rich in Pu. The content of Pu tended to increase in muscle of pike with the increasing size of the fish. Activity concentration of 137Cs (Bq∙kg− 1 d.w.) in muscle of pike, a piscivorous fish, 7.74 ± 5.12, was significantly higher (p < 0.001) than the average activity concentration of 137Cs in muscle of dace, 2.51 ± 1.57, and grayling, 2.50 ± 1.71. This can be attributed to biomagnification of cesium in food nets. The results will draw a baseline for assessment of dose-dependent ecological risks for wild fish itself and fish consumers.