So far, in the design and operation of drainage systems insufficient attention has been paid to the stage of operations during the possible water volume changes. We are offering mathematical modeling methods for more accurate selection of parameters of multiple nature-technology systems, a significant increase in project quality and avenues to developing new technological solutions. We present models, algorithms and programs for numerical modeling of filtration flows under hydraulic facilities. Such tasks should be solved while designing and optimization of parameters of hydraulic facilities. Numerical algorithms are based on the finite element method. The results of computational experiments confirmed the high accuracy of numerical algorithm.