The research was aimed at identifying groundwater contaminants in the inflow area of the Gdańsk intakes of “Czarny Dwór” and “Zaspa Wodna”, and determining their origin. The hydrochemical study covered an area of over 12 km2; it also included the vertical variation in the chemistry of the aquifer. The study shows that the most common parameters decreasing the water quality are typical municipal sewage components, communication pollutants and, locally at several locations, compounds derived probably from some industrial plants or service facilities.In most of the area, the poor groundwater quality in the upper part of the aquifer, caused by anthropogenic influence, does not affect the quality of water in the central and lower parts of the aquifer. However, the water is mixed near the intakes, because of the induced groundwater inflow from the entire vertical section to the active wells. Migration of VOC compounds, which are heavier than water and gradually sink toward the aquifer's bottom, occurs in a different way. Based on a hydrochemical model, a prognosis of the time and direction of contaminants migration has been made.