In the practice of water management for economic purposes, calculations of suspended sediment for various time scales – from per-second to annual, are important. The estimation of annual suspended sediment transport, as well as of the statistical parameters of turbidity and the reliability of the estimates, is extremely difficult because of irregular and insufficient light conditions in different phases of the water regime. At the same time, owing to the knowledge of the processes that shape the quality of natural waters and a sufficient toolkit of calculation methods, the main indicators of water quality with can be reproduced with acceptable accuracy. The capabilities of statistical analysis of water quality indicators can be expanded by an integrated approach to estimating the indicators by means of well-proven deterministic and stochastic calculation algorithms with arguments observed regularly and for a long time. In this case, a composite method can be used to estimate the parameters of the suspended sediment distribution or water turbidity, which permits finding the parameters of the distribution curve of the function from the parameters of the distribution curve of its arguments. The paper presents a deterministic-stochastic modeling system “weather-runoff-suspended sediments”, based on a stochastic weather model, a model of runoff formation in a catchment area, and a model of annual suspended sediment transport. The system can estimate the distribution parameters of daily suspended sediment load and turbidity values in the situation of observed data shortage or changes in runoff formation in the catchment resulting from natural causes or economic activities.