The software System for Simulation Modeling of Water Bodies, which was developed at the V. M. Glushkov Institute of Cybernetics of NASU, includes the subsystems for modeling changes in the oxygen mode and pollution transport by watercourses, filtration processes in underground water-bearing horizons, flow states in water reservoirs, and an intelligent method for processing, compressing, and recovering arrays of numeric data with a guaranteed accuracy using the apparatus of the best Chebyshev approximation applied in all the subsystems. Models for some water bodies of Ukraine are created for the first time. The System is extensible, i.e., is open to include new models and objects. The subsystem of modeling water flows in water bodies is described in more detail.