The development of animal husbandry on an industrial basis causes a sharp increase in the amount of highly polluted wastewater, the purification and disinfection of which is one of the most important tasks when deciding on their use in agriculture as fertilizer or discharge into reservoirs or irrigation fields. The effectiveness of such systems is achieved with the help of new ways of processing information and mathematical characteristics of technology processes. Based on the study of the main methods of creating discrete chemical and technological systems (CTS), the expediency of using the design of Petri nets (SP) to simulate the process of wastewater treatment of livestock farms (OSWF) was developed. To characterize the system, we use N–schemes, which are based on the mathematical system of the joint venture, which can form a network structure both in analytical form for automating work during analysis, and in graphical form to create visibility of the created model. Analyzing technological and chemical processes, it is important to take into account the formality condition of N–circuits, which assumes that the circuits do not take the properties of simulated systems in time, since the timing of the transition is taken to be zero. We took into account these conditions and proposed updated Petri nets that are focused on the analysis and simulation of discrete CTS, by changing the time delay of labels on transitions and positions, as well as by enabling transitions that are in priority. We have created a model in the form of a modified updated Petri net (SME). With the help of SCADA TRACE MODE technologies, we have developed a whole software package for the control system in the process of OSWF. This system can perform dispatching monitoring of the main parts of the control apparatus, as well as stop and analyze and monitor its condition, this is feasible both in general and within the framework of forecasting the occurrence of emergency situations.