The article discloses the main areas of institutional support for sustainable ecological and economic development of economic entities on the basis of conceptual approaches to the systematization of methods and mechanisms for the protection of their economic interests. There described the mathematical basis of Petri nets used in the modeling and design of the module bioremediation of hydrocarbon wastewater. There described the technique of two-tier system of the modeling process of biochemical treatment of oily wastewater, as well as a model developed by the authors in the form of a modified Petri nets and software package management system of biochemical treatment of wastewater