The questions about optimization of technological systems of sewage treatment of the dairy industry are considered. On the basis of the system analysis principles of construction of mathematical models and the choice of methods of calculation of optimum variants for definition of clearing constructions structure are developed. On the example interdependence of a clearing constructions complex it is shown, that change of any of parameters of work of each construction conducts to change of operating conditions not only it, but also all technological chain. The developed basic approaches to mathematical modeling separate constructions and their interconnected complexes allows to execute optimization of sewage treatment systems in dairy industry and to receive significant economic and ecological effect.