While developing hydrocarbon (oil and gas) deposits, it is necessary to drill into shallow formations of fresh (drinking) water, and this causes the filtrate invasion from the open wellbore into these formations. A mathematical model of this process was created; an analysis of the influence of the identified by the process features filtration zones was performed, and it was shown that the zones of the mud crust and interstitial colmatation are dominant. The filtrate invasion can significantly impair the quality of fresh water and cause environmental damage.