The western part of the Drava alluvial aquifer system, located in northern Croatia, contains significant amounts of groundwater, which is primarily used for public water supply and irrigation. The groundwater of this system contains high concentrations of nitrate which is why aquifer system is classified as a groundwater body of poor chemical status under the Water Framework Directive (WFD). We investigated the groundwater age in this aquifer system and compared the nitrate concentrations in groundwater and the nitrogen pressure from agricultural activity with respect to the estimated mean groundwater age. We used a combination of the environmental tracers: chlorofluorocarbons (CFCs: CFC-12, CFC-11, and CFC-113), sulphur hexafluoride (SF6), tritium (3H) and noble gases. By applying lumped parameter models, we determined the groundwater age in aquifers at different depths. On comparing the recharge year, historical data on nitrate concentrations in groundwater, and nitrogen pressure from agricultural activity, we found that these elements are closely related. Our investigation was also supported by the results of numerical simulation of the evolution of nitrate concentration in the saturated zone of the aquifer. The decrease in agricultural pressure caused a decrease in the nitrate concentrations in the youngest, shallow, and oxic groundwater. However, the trend of increasing nitrate concentrations in the deeper part of the aquifer can last for many years. Our research supports the thesis that groundwater age is an important criterion for assessing the effectiveness of protection measures taken in groundwater management and implementation of the WFD and Nitrate Directive.