Aquatic organisms at Chernobyl have now been chronically exposed to environmental radiation for three decades. The biological effects of acute exposure to radiation are relatively well documented, but much less is known about the long-term effects of chronic exposure of organisms in their natural environment. Highly exposed fish in freshwater systems at Chernobyl showed morphological changes in their reproductive system in the years after the accident. However, the relatively limited scope of past studies did not allow robust conclusions to be drawn. Moreover, the level of the radiation dose at which significant effects on wildlife occur is still under debate. In the most comprehensive evaluation of the effects of chronic radiation on wild fish populations to date, the present study measures specific activities of 137Cs, 90Sr, and transuranium elements (238Pu, 239,240Pu, and 241Am), index conditions, distribution and size of oocytes, as well as environmental and biological confounding factors in two fish species perch (Perca fluviatilis) and roach (Rutilus rutilus) from seven lakes. In addition, relative species abundance was examined. The results showed that both fish species are, perhaps surprisingly, in good general physiological and reproductive health. Perch, however, appeared to be more sensitive to radiation than roach: in the most contaminated lakes, a delay of the maturation of the gonads and the presence of several undeveloped phenotypes were evident only for perch and not for roach.