An avenue to integrate theoretical, experimental and field research methods to forecast water quality in water bodies for different scenarios of water management is proposed. Exploration of the laws of organization, stability and controllability of laboratory "ideal" water microbial communities (model ecosystems) is the basis to build the following biophysical research chain:to formalize with primary field information a conceptual block-diagram of a water ecosystem →to real chemical and other density-dependent and population-growth-controlling factors → to find our limiting factors for natural ecosystems → to conduct experiments with isolated chemical factors and hydrobionts to derive kinetic dependencies and quantitative parameters→ to transfer regularities of operation and kinetic dependencies to the natural ecosystem→ retrospective verification of the model on the base of available field and derived theoretical-experimental data →prognostic calculations for the scenario. Efficiency of the approach is demonstrated in microalgal "blooming" models for Krasnoyarsk and Kantat reservoirs and in prognostication of radioecological state of great Yenisei river:1) radionuclide distribution in the Yenisei's bottom sediment is nonuniform-"spotty"; 2) it is theoretically shown, that due to biological interactions and tro-phical radioniclide migration there is "spotive" type of space radionuclide distribution. The research is to make use of the novel methods of ecological biophysics:Monitoring:spectral analysis of surface waters (algal pigments), fluorescent techniques to evaluate productivity and condition of algae; rapid bioassays for water toxicity (bioluminescence, chemotaxis techniques). Kinetic experiments:microcosms on evaluating self-purification rates; special cultivators to evaluate the rates of growth of hydrobionts and radioactive engulfing, nutrition spectra; methods of finding growth limiting factors. Models:application of Bellman Principle to optimizing the river water use; theory and peculiarities of microbiological decomposition of pollutants in the river ecosystem. The composition of Prognostication Simulation Model is the next:1) hydrodynamical unit to calculate 2-dimensional space-time rate of stream on any depth; 2) hydrophysical unit to calculate:water temperature and level of solar radiation inside the water body; 3) ecosystem unit to calculate dynamic of concentration of phytoplankton, zooplankton, bacteria, major chemical matters and pollutants in water, content pollutants inside of hydrobionfs cells and dynamic of bentos; 4) radioe-cological unit to forecast the dynamic of radionuclides in the water body and bottom, their hydro-bont's concentration; 5) database. Reservoirs and river models are provided by monitoring and kinetic experiments data.