This article presents the Software as a service system that allows creating scenario modeling of pollution transfer for diffuse sources of pollution using the example of the Ili river basin (Republic of Kazakhstan). The development of technologies that determine hydrological state of the lake and water in it are analyzed. The practicability of modeling the discharges and distribution of pollutants is substantiated. The FORTRAN Hydrological Simulation Program software, a computer model that allows us to model the concentration of nitrate compounds (NO3), total ammonium, and biochemical oxygen consumption with one day time resolution for the period from 1980 to 2016 was described. The model was calibrated using the field observations data from 6 hydrological posts, which made it possible to obtain satisfactory water discharge values. To work with the system, a graphical interface was developed which allows the user who is not familiar with the FORTRAN Hydrological Simulation Program software to make calculations. Implemented was an algorithm for automated starting of scenario calculations with post-processing and presentation of results. The web-based approach facilitates multi-user, one-time and fast access to the system from anywhere in the world. The efficiency of results of programming was investigated and the dynamics of changes after using the FORTRAN Hydrological Simulation Program software was established.