The occurrence and mitigation of selected pesticides and nitrates in surface and groundwater samples from two alluvions in the Republic of Serbia are investigated in this study. The influence of aquifer conditions on the degradation processes of pesticides and nitrates is considered as a potential removal mechanism of compound residues in alluvial groundwater. Nitrate concentration was analyzed in 144 groundwater samples in the Kovin-Dubovac drainage system and 63 samples at the Ključ groundwater source. The occurrence of 15 pesticides was monitored in groundwater in a total of 34 samples in the Kovin-Dubovac area and 14 samples at the Ključ groundwater source. Concentrations of selected pesticides and nitrates were monitored in eight samples from the Danube in the Kovin-Dubovac area and 15 samples from Velika Morava at the Ključ groundwater source. Both selected locations are agricultural areas. Results show that concentrations of nitrates (NO3−) are much higher in oxic groundwater conditions compared with concentrations in typical anoxic conditions. The opposite is the case for the concentration of pesticides that occurred in surface and groundwater samples. These results are very important for a better understanding of the self-purification potential of alluvial aquifers and assessment of aquifer condition influence, especially oxic or anoxic conditions, on the occurrence and mitigation of selected agrochemical residues in groundwaters.