Multivariate statistical techniques were applied to evaluate spatial/temporal variations, and to interpret water quality data set obtained at Alqueva reservoir (south of Portugal). The water quality was monitored at nine different sites, along the water line, over a period of 18 months (from January 2006 to May 2007) using 26 water quality parameters. The cluster analysis allowed the formation of five different similarity groups between sampling sites, reflecting differences on the water quality at different locations of the Alqueva reservoir system. The PCA/FA identified six varifactors, which were responsible for 64% of total variance in water quality data set. The principal parameters, which explained the variability of quality water, were total phosphorus, oxidability, iron, parameters that at high concentrations indicate pollution from anthropogenic sources, and herbicides indicative of an intensive agricultural activity. The spatial analysis showed that the water quality was worse in the north of the reservoir.