In the regional recharge zone of a Quaternary groundwater flow system distinct groundwater contamination was investigated, reflected mainly by high nitrate concentration. The main objectives of presented study were the investigation of the behaviour of nitrate in relation to the flow system and the documentation of the denitrification processes. The examination of groundwater chemistry was performed using data from dedicated groundwater sampling and studies, measurements of the gaseous N2 dissolved in the groundwater and also tritium analyses. The distinct groundwater contamination was detected in the near-surface zone of the unconfined aquifers, indicated mainly by high nitrate concentrations (>+70 NO3mg l). These contaminants migrate to the deeper parts of the flow system at the regions of intensive groundwater exploitation, where concentration of nitrate at depth of 80 m exceed 10 NO3mg l. In the regions where the water extraction is not performed the nitrate concentrations are low, even if in the shallow part of the aquifer the concentration of nitrate exceed 70 NO3mg l. Low nitrate concentrations occur also in the regions of confined aquifers occurrence. It was detected with use of gaseous N2 measurement that denitrification is the process of nitrate removal from groundwater. The potential for denitrification is higher in the confined conditions and leads to an overall decline in nitrate in the deep aquifers. Based on research performed the conceptual model of groundwater circulation was formulated. It was documented that the recharge areas are extremely vulnerable to pollution by nitrate. It was also concluded that the monitoring of groundwater chemistry should be performed for both shallow and deep parts of the flow system, even though the shallow part is not used for water supply purposes. This work was made possible by the financial support of the Ministry of Science and Higher Education (grant no. 2164 BT02 2007 33) and by support of the National Science Centre Poland (grant no. 2014 15 B ST10 00119)< p>