In this paper the concept of filtration and the problem of microbial contamination occurring in the fuels and oils was presented. Then the factors influencing the growth of bacteria in petroleum products were described in detail. In the next part of the article modeling of the impact of fuel microbial contamination on filtration efficiency was performed. The modeling presented in the article is an example showing how undesirable phenomenon is the microbial contamination and how pollution affects the other elements of the entire system. As part of the modeling, numerical model of filtration with the solution was presented. Then analysis results on the basis of the impurities concentration characteristics in the fuel as a function of the fouling thickness in the partition of the filter is performed. The development of impurities was divided into three stages. In the article for one case the trend line was presented. The article was completed conclusions.