Trace element concentrations in water from São Francisco River using Particle Induced X-ray Emission (PIXE) and Synchroton Total Reflection X-ray Fluorescence (STXRF) techniques are measured. The main objective of this work was to characterize and to monitor the trace elements in the water of São Francisco River, as well as to provide valuable information about the levels of metallic ions pollutants. Water samples were collected monthly at five locations along the course of the river from July 2003 to April 2004. As an internal standard, 11.6 ppm of Yttrium was added to 10 ml of the water sample. The PIXE and TXRF measurements were performed at the Ion Beams and Materials Laboratory (LAMFI) and the Brazilian National Synchrotron Light Laboratory (LNLS), using a proton beam and a polychromatic X-ray beam, respectively. Si(Li) detectors were used to collect the X-ray spectra. Due to the excellent detection limits of the PIXE and STXRF analysis, up to 15 elements were quantified. The highest total content of Cr, As, Cu and Zn detected in river water are above the limits recommended by the environmental legislation.