Resumo. Abstract: Aim This study characterized the water quality in the lower São Francisco River (NE-Brazil).This research represents the first work to be carried out in the lower sector of the São Francisco river aiming to quantify and compare limnological variables, during three different years (2001, 2004 and 2007). Methods Water samples were collected in a transversal section of the river at monthly intervals period on surface layer. Temperature, conductivity, pH, and dissolved oxygen were obtained using a multiparameter probe YSI-6600. The dissolved inorganic nutrients (ammonium, nitrite, nitrate, dissolved phosphorus and silicates), chlorophyll-a and total suspended sediment (TSS) were also determined. Results The three hydrological years showed differences in precipitation rates and discharge conditions. The year 2001 had precipitation rates below the historical series of rainfall. The mean annual water temperature showed negligible differences among the three years. Dissolved inorganic nutrient concentrations were highest in 2004, with ammonia and nitrate differing statistically between the years (p<0.05); the later showed the largest concentration of dissolved inorganic nitrogen. Chlorophyll-a showed a slight difference among years. Conclusions Precipitation intensity has a direct impact on the São Francisco River discharge, but the geographical distribution of the precipitation is also a determinant factor for alterations of the chemical and physical characteristics of the water that reaches the lower sector of the São Francisco River.