The Raigón aquifer is an important groundwater system in southern Uruguay. The increasing use of groundwater resources in the last decades has provoked changes in the concentration of many elements which are strongly related to anthropogenic pollution sources. Concentration levels are useful to detect changes in reservoir status but it is also necessary to analyze their chemical significance in order to make an accurate assessment of the sources of contamination and the causes of changes. In this work we use the available thermodynamic data to calculate chemical speciation on these groundwater samples. Trace elements present as anions, in particular Se and Mo, are especially focused to show the chemical modeling possibilities. Both elements form anionic species, predominantly MoO42- and SeO42-. Results show that these anions interact in solution and are greatly influenced by the concentration of the abundant calcium ion. Localized changes in pH can strongly affect the situation. The same is observed with the pE parameter, but only in the case of Se. Chemical speciation of trace elements is in general highly dependent on pH, pE and concentration of major elements. In consequence, for a fixed analytical total concentration, these parameters can markedly change the situation, affecting the mobility, the bioavailability and environmental fate of these elements. The strategy employed in this work can also be extended to the study of many other environmental water scenarios.