The nitrogen compounds, namely ammonium, nitrite and nitrate nitrogen, are the main substances polluting the quarry and drainage waters of mining enterprises that use the ammonium nitrate-based explosives for drilling-and-blasting rock mass preparation. In accordance with the legislation, such waters are subject to treatment prior to discharge into the water bodies. At the mining enterprises, the promising treatment method is the treated water conditioning in the flooded abandoned open-pit mines, during which the natural microbiological nitrification of ammonium and nitrite nitrogen contained in the quarry drainage waters is performed with an efficiency of more than 95%. The article discusses the influence of natural climatic and hydrodynamic factors on the nitrification process according to the results of a purification process study that has been performed since 2014 until the present time at a large mining enterprise. The relevant conclusions and recommendations are given.