An overwhelming part of fresh waters is concentrated in environmentally sensitive small rivers, lakes and swamps. A complete lack of control over their state coupled with the poor economic development of the Arctic zone threatens to lead to large-scale regional and interregional disasters. The article presents an approach to the organisation of a system of control over the ecological state of fresh waters, based on the regularities and generalizations obtained by research and design organisations based on many years of research. It is proposed to locate observation points at reference water bodies selected on the basis of landscape-hydrological zoning of the controlled territory. The set of signal indicators determined at these points will consist of a small number of integral hydro-chemical parameters of water quality which allow describing the formation and development of negative ecological intra-water body processes, as well as, in general terms, the socio-economic consequences of these processes. In general, the proposed approach is the basis for the organisation of a signal system of freshwater monitoring aimed at informing the environmental authorities in advance about the need to take preventive measures to avoid a large-scale environmental crisis.