There is old-established avowed demand of determination of ecologically proved limits of anthropogenic impact at natural ecosystems. Preservation of fresh waterbodies and streams ecosystems is very essential problem, because the fresh water more and more becomes one of the most important strategic resources. Of course, sea ecosystems are also needed in protection owing to their role in the biological resources maintenance. A monitoring system includes complex of different hardware and software, which must ensure forehanded discernment of a natural object state, the state assessment and forecast of the object critical situations. It is evident, that prophylaxis of a sickness is better than its therapy, and the therapy is most successful at the earliest stage of the sickness. Many scientists characterize the present-day state of the biosphere as the state of global ecological crisis. The main reason of the crisis consists in poisoning of the biosphere by toxic products of humanity activity. These products directly affect at physiological processes of organisms. The toxic contamination combines with intake into ecosystems anthropogenic substances of the total ecological influence. These substances do not directly affect at the organisms but the substances accumulation leads to non-marginal changes of the ecosystems biogeochemical cycles. In turn, the changes lead to reorganization of the ecological community structures, substitution of the dominants and edificators. Anthropogenic eutrophication is the main example of such influence for aquatic ecosystems. The eutrophication occurs due to additional intake of phosphorus and nitrogen in mineral forms and as a part of organic matter. The paper presents some results of computer simulation research of the present-day monitoring system capability to reveal changes in aquatic ecosystems.