Contamination from agricultural sources and, in particular, nitrate pollution, is one of the main concerns in groundwater management. However, this type of pollution entails the entrance of other substances into the aquifer, as well as it may promote other processes. In this study, we deal with hydrochemical and isotopic analysis of groundwater samples from four distinct zones in Catalonia (NE Spain), which include different lithological units, to investigate the influence of manure fertilization on the overall hydrochemical composition of groundwater. Results indicate that high nitrate concentrations, resulting from intense manure application, homogenize the contents of the major dissolved ions (i.e.; Cl-, SO42-, Ca2+, Na+, K+, and Mg2+). Moreover, positive linear relationships between nitrate and some ions are found indicating the magnitude of the fertilization impact on groundwater hydrochemistry. Nevertheless, the increasing concentration of specific ions is not only attributed to the manure input, but to the enhancing effect of manure and slurry upon the biogeochemical processes that control water-rock interactions. Such results raise awareness that such processes should be evaluated in advance in order to assess adequate groundwater resources assessment