Proton-Induced X-ray Emission (PIXE) technique has been employed to determine elemental concentrations in surface water samples collected from some rivers and streams in zones affected by human activities, as well as underground water samples (well and tap water) from different localities in Romania. The sampling points were located both in areas with various industrial and agricultural activities and in control zones. PIXE analyses have been carried out using a 3 MeV proton beam, generated by the 9 MV FN Van de Graaff Tandem accelerator at Horia Hulubei National Institute of Physics and Nuclear Engineering in Magurele (near Bucharest). The target was placed in vacuum in the center of the irradiation chamber at 450 angle with respect to the incident beam and X-ray detector (Si(Li) Ortec, FWHM of 180 eV at 5.9 keV). The proton beam current on the target was ~0.5 nA. As targets, volumes of 200-250 μL were pipetted on Mylar foil (2.5 μ thickness), dried at room temperature, then fixed on special aluminum frames (2x3 cm2). Yttrium (Y) internal standard was used as proton beam flux monitor. GUPIX (Guelph PIXE) program was employed for spectra processing (thin targets). Certified Reference Materials (CRMs), prepared in a similar way with the investigated samples, were considered for quantitative analysis: CRM-TMDW (drinking water); CRM-OT (oyster tissue); IAEA-V10 (hay); IAEA-393 (algae); IAEA MA-B-3/TM (fish homogenate). PIXE technique allowed the determination of the concentrations of elements Al, Si, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, As, Br, Rb, Sr, Hg and Pb in water samples. The obtained results were compared with literature data, Romanian admissible levels of chemical elements in surface water, and WHO concentration limits for potable water. For some water samples, the results obtained by PIXE were compared with those obtained by complementary analytical techniques, such as neutron activation analysis or atomic absorption spectrometry.