The creation of reservoirs has a transforming effect on the landscape of river valleys in connection with a change in the earlier existing regime of surface and ground waters. Of the geological features of these valleys, the one most sensitive to a change in the regimes of flooding and moistening is the soil-cover complex, a change in the state of which makes it possible to predict subsequent links of the ecological chain and to develop nature conservation measures. In the case of stream flow regulation the greatest damage is inflicted on the soil-cover complex by flooding of territories, which leads to death of the vegetation that existed earlier. In this paper the effects of flooding and stream flow regulation as well as the resulting subirrigation by groundwater on the soil-cover complex are described and measures are developed for nature conservation in flood plains and deltas.