Based on the assumption that the water quality in a watershed is directly related to the degree of equilibrium between the natural and anthropic factors, in this paper we examined the effects of the land cover changes in areas of savanna (Cerrado biome) over the watersheds ecological viability (expressed here as Water Quality Index). Thus, we analyzed two middle-sized basins located in the Goiás State (a representative area of this biome), with different characteristics regarding both the physical aspects (soil, topography and remnant vegetation) and human aspects (environmental degradation level and economic development index): (1) João Leite basin, located in the Center-South State (anthropic level = 88%), and (2) São Domingos basin, in the Northern State (anthropic level = 25%). Chemical analyses have indicated that the water in the São Domingos basin presents, in general, a better quality for human consumption and for the ecosystem maintaining, reflecting the high conservation state of this basin as well.