The state of knowledge about the study of the hydrophysical processes and ecosystems of large lakes and the White Sea are considered. The data are presented that are needed for obtaining new knowledge necessary to create basic numerical models for predicting ecosystem changes with calibration and verification of numerical models. The advantages of setting up specialized surveys at research polygons in the lakes and the White Sea are demonstrated compared to organizing such experiments in the ocean. Both the traditional approaches to modeling physical-chemical-biological processes, and innovative developments for describing aquatic ecosystems where knowledge is lacking are represented, e.g. for the ice-covered winter conditions using so-called finite automata method. Ecosystem change estimates are suggested, to be applied for sustainable management and conservation of the resources of waterbodies. Information about the application of the cognitive approach in describing the socio-ecological-economic processes in the waterbody-catchment system is provided. The necessity of creating multipurpose polygons to create advanced technologies in the field of hydrology, oceanology, meteorology and climatology, and improvement of the monitoring system is substantiated. It is argued that the resources and capacities of various organizations need to be united to arrange integrated experiments and build models for dealing with the tasks of the rational management of internal waters.