Cryptosporidium and Giardia are pathogenic agents which cause risk to public health. The goal of this research was to evaluate the risk of infection by cryptosporidiosis and giardiasis in a population of the Cerrado biome and its relation to land use. Raw water samples were collected from 41 different surface sources of the state of Goiás (Brazil). The parasites were quantified via the membrane filtration method. The probability of an individual contracting an infection after consuming contaminated water was estimated using the quantitative microbial risk assessment. Generally, the analyzed watersheds (WS) presented Giardia cysts in 63.4% of the samples (<LD at 116.67 cysts/L) and Cryptosporidium oocysts in 87.8% of the samples (<LD at 300 oocysts/L). The WS with pasture predominance were statistically associated with the presence of Cryptosporidium, in which the possible contamination source is the excrements of animals. There is a greater risk of giardiasis. It is concluded that there is a need to implement improvement actions regarding environmental quality and the management of the use and occupation of surface sources in the Cerrado Biome, in order to reduce the spreading of diseases and negative impacts to the local population.