In this work the analysis of elements concentration in groundwater was performed using the synchrotron radiation total-reflection X-ray fluorescence (SR-TXRF) technique. A set of nine tube-wells with serious risk of contamination was chosen to monitor the mean concentration of elements in groundwater from the North Serra Geral aquifer in Santa Helena, Brazil, during 1 year. Element concentrations were determined applying a SR-TXRF methodology. The accuracy of SR-TXRF technique was validated by analysis of a certified reference material. As the groundwater composition in the North Serra Geral aquifer showed heterogeneity in the spatial distribution of eight major elements, a hierarchical clustering to the data was performed. By a similarity in their compositions, two of the nine wells were grouped in a first cluster, while the other seven were grouped in a second cluster. Calcium was the major element in all wells, with higher Ca concentration in the second cluster than in the first cluster. However, concentrations of Ti, V, Cr in the first cluster are slightly higher than those in the second cluster. The findings of this study within a monitoring program of tube-wells could provide a useful assessment of controls over groundwater composition and support management at regional level. © IWA Publishing 2012.