Increased reliance of urban populations on Rio Grande water has necessitated an expanded microbial surveillance of the river to help identify and evaluate sources of human pathogens, which could pose a public health risk. The objectives of this study were to investigate microbial and chemical water quality in Rio Grande water and to perform risk assessment analyses for Cryptosporidium. No oocysts in any of the ten-litre samples were detected. However, the limit of detection in the water samples ranged between 20 and 200 oocysts/100 L. The limits of detection obtained in this study would result in one to two orders of magnitude higher risk of infection for Cryptosporidium than the U.S.EPA annual acceptable risk level of 10−4. The bacterial data showed the significance of animal farming and raw sewage as sources of fecal pollution. Male specific and somatic coliphages were detected in 52% (11/21) and 62% (24/39) of the samples, respectively. Somatic coliphages were greater by one order of magnitude, and were better correlated with total (r2=0.6801; p≤0.05) and fecal coliform bacteria (r2=0.7366; p≤0.05) than male specific coliphages. The dissolved organic carbon (DOC) and specific ultraviolet absorbance (SUVA) values ranged 2.58–5.59 mg/L and 1.23–2.29 m−1 (mg/l)−1, respectively. Low SUVA values of raw water condition make it difficult to remove DOC during physical and chemical treatment processes. The microbial and chemical data provided from this study can help drinking water utilities to maintain balance between greater microbial inactivation and reduced disinfection by-products (DBPs) formation.