Paper presents the development conceptual, mathematical and computer models of wastewater purifying system of organic matter. The conceptual model was developed as a Diagram Cycle Activity and Cause-Effect Diagram. The mathematical model is set up based on the system of differential-difference equations. The Runge-Kutta method was using to solve equations system. Computer model was created by Powersim Constructor v. 2.51. In each system’s component, using the Runge-Kutta method, generates the difference equation.

A computer model for variable uses randomly chosen values from the theoretical probability distribution of variable was applied. For the validation of the model, as the distributions are asymmetrical non-Gaussian distributions, applied non-parametric test.

For two independent samples was used to rank sum test (the Mann-Whitney U-test). After proving that the model describes well the actual system is designed experiment with concentrations of organic matter in the unpurified food industry wastewater.