We consider some experience of computer simulation of within-year cycles of aquatic ecosystems, which has group of lecturers and scientists of St. Petersburg State University. The experience includes designing point, reservoir and spatially non-homogeneous simulation models of aquatic ecosystems functioning, and carrying out numerical experiments with the models. The models are applied for investigations in the sphere of ecology, nature protection and nature management. Main attention in the report is devoted up-to-date state of the simulation.