Monitoring of aquatic objects ecological state must include forehanded recognition of critical situations. Therefore, the forecasting widely uses possibilities of computer simulation. Of course, the most complicated and relevant simulation model of an aquatic ecosystem is giant simplification of its real life. Nevertheless, history of mathematical ecology proves that even such simple simulations of population dynamics, as predator-prey models and ones of competition for a resource between two or three species can give new knowledge in sphere of synecology. The main modern global hazard for the Earth biosphere is its poisoning by anthropogenic toxicants. Aquatic ecosystems are also exposed by danger of anthropogenic eutrophication due to additional income of nitrogen and phosphorus. However, the anthropogenic toxic pollutants are often observed in aquatic objects at a low concentration, which cannot be toxic for the hydrobionts. On the other hand, many of the toxic substances are liable to accumulation within in organisms of the hydrobionts, especially the ones of the upper storeys of the trophic pyramids. Therefore, we can come up against a situation, when the monitoring shows low non-dangerous concentration of a toxic substance in a waterbody, but the ecosystem hydrobionts have very high and dangerous concentrations of the substance. Situation with the eutrophication monitoring is alike. Concentrations of nitrogen and phosphorus in mineral and organic forms in aquatic ecosystems are non-dangerous for hydrobionts. The main results of the anthropogenic eutrophication, which jeopardize the aquatic ecosystems, are discharge of toxins by blue-green algae and depletion of dissolved oxygen after “bloom” of the phytoplankton. Therefore, there is total problem of aquatic ecosystems monitoring. The problem consists in the fact that the observed characteristics often cannot give information for recognition and forecasting of critical situations with an aquatic ecosystem, and determination of its ecological state. The article is devoted to revealing of the aquatic ecosystems parameters, which are the most informative ones for decision of the ecosystems ecological state and their emergent peculiarities based on composite indexes. The revealing has been carried out by means of computer simulation. The parameters can be used at the aquatic ecosystems monitoring.