Presented are the results from summarizing many years (1990–2012) routine hydrochemical data on content of cadmium and lead compounds in river ecosystems of different natural zones and altitudinal belts of Russia. This study used data on chemical composition of water from 91 observation posts on 75 rivers. Long-term variability in content levels of metals is considered with respect to the ranges of variation in concentration of a long-term period, median values of concentration and the MAC exceedance frequency. It is shown that in different natural zones and altitudinal belts, the content level of cadmium compounds is relatively uniform and varies from values below the detection limit to 39–45 μg/dm3 in most of the river ecosystems used in this study. The content of lead compounds in the river water varies over a broad range, from zero values to 44 μg/dm3 (except for anomalously high concentrations in separate river ecosystems). And the highest values are observed in the rivers of the taiga zone. An assessment is made of the pollution level of the river waters by lead and cadmium compounds. The largest number of cases of high and extremely high water pollution was recorded for lead compounds. The proportion of the river ecosystems with a high and extremely high level of water pollution by cadmium and lead compounds constituted 21.2 and 46.9 %, respectively. It was found that not only does the presence of cadmium and lead compounds in aquatic ecosystem deteriorate the water quality and the state of aquatic ecosystems, but it also disturbs the functioning of hydrobionts. Therefore, results from assessing long-term variability in contents of the most dangerous heavy metals, lead and cadmium, in the water environment can be used in developing measures for water quality improvement and for recovery of the status of river ecosystems.Keywords: MAC exceedance ratio, MAC exceedance frequency, high pollution level, priority pollutants, heavy metals, cadmium and lead compounds.