In this study, nutrients, trace metals and priority pesticide compounds were investigated for the first time in water and sediment samples in streams of the Evrotas River basin (S.E. Greece) from 2006 to 2008. The most important sources of contamination were from the entry of pesticides and nutrients into surface waters and sediments as a result of the intensive agricultural activity as well as from the uncontrolled disposal of olive mill and citrus processing wastewaters. Aquatic risk assessment revealed that all insecticides detected showed high risk, suggesting adverse effects on the stream biota. Among the metals analyzed, Cr, Ni and Ba presented the highest concentrations in sediments, however, due to natural geological processes. Multivariate statistical techniques applied for data compression, exploration and interpretation proved to be useful tools for identifying the most critical pollutants affecting the surface water quality. The findings of this study suggest that the inclusion of streams with small catchment areas into WFD monitoring and assessment programs is essential, especially those of the Mediterranean region.