A new approach for modeling complicated nonlinear processes, including processes of self-organization, using so-called cellular automata is suggested. A computer model of the distribution of persistent impurities, assessment of pollution and thermal regime of Lake Ladoga was built as an example. Modeling problems are solved successively from simple to more complex ones: from a zero-dimensional vertical model of the lake’s deep-water area to a two-dimensional model for the lake’s longitudinal section and, finally, three-dimensional model of the entire water body. The generated models are designed so that they can be further expanded to include hydrochemical and hydrobiological variables for simulating lake ecosystems.