Based on the phenetic analysis of non-metric features of the skeleton and the geometric morphometric methods of the cleithrum shape the author analyzed the differences among the perch populations in the South Urals in conditions of increased water mineralization and chronic radioactive pollution (over 50 years). Water mineralization had a greater morphogenetic effect than the chronic radioactive pollution. The variability of the cleithrum shape in the perch from reservoirs with different water mineralization 4.7 times exceeded that caused by radioactively polluted environment. The phenotypic shift in the perch from the lake Kozhakul’ (increased water mineralization) compared to the perch from the lake Irtyash (low water mineralization) was much greater than in the groups inhabiting ponds of the Techa cascade where radioactive waste is stored. In the gradient of higher radioactive impact in the Techa tandem reservoir system we marked an increased total number of morphogenetic aberrations in the skeleton structure.