We examine the influence of groundwater flow patterns and denitrification on nitrate migration in a regional recharge zone. It has been shown that nitrate contamination has a different behaviour in regions where groundwater is exploited (where deep percolation of nitrate takes place) than where natural gradients exist (with no deep aquifer zone contamination). Multicomponent chemical tracers and isotopic methods were used in the investigation. A contaminant plume was discovered in shallow parts of the aquifer which percolated into deeper parts of the flow system in those regions with a downwards gradient induced by groundwater withdrawal, where the influence of denitrification was limited. Local conditions leading to intense denitrification, i.e., local changes in geological conditions (low-permeability silt intercalations), were also documented. Therefore, vertical changes in groundwater chemistry should be examined to ensure groundwater resource management and protection, as these are extremely important in regional recharge zones with a downwards gradient.