In the paper, the issues of provision the sustainable functioning of the ecosystems (natural-engineering systems) of the catchment area of small rivers were considered. It was distinguished, that one of the most widespread kinds of impact is land-destructive load, associated with direct expropriation and transformation of lands, occupied by natural ecosystems. The authors present the criteria for regulation of the land-destructive load, based on the assessment of the diversity of natural and anthropogenic-modified ecosystems in the catchment area of a small river. It was found, that a part of anthropogenic-modified ecosystems should not exceed 35–40 % of the total catchment area (for the middle and southern taiga zone).