This study evaluates the quality and pollution status of source surface waters in Segou, Mali. The nature, sources, and extent of pollution of Comatex Stream, Cerfitex Pond, and Sonikoura River were studied for a period of twelve months (July 2016–June 2017). Analysis included 209 water samples collected from eleven different locations in the study area. Laboratory and field analysis were realized using the standard methods and concerned eleven parameters including four physicals, six chemicals and one bacteriological. Also, organoleptic parameters were observed. Most of the average values of parameters addressing the quality of water were significantly higher (P < 0.05) in both the stream and river compared to the pond. Fecal coliform counts (FCC) were not in significant correlation with the temperature; pH and turbidity; but had a significant and positive correlation (P < 0.05) with conductivity: total dissolved solids (TDS); total suspended solids (TSS); Cl−; PO4−P; NO3−N and 5-day biochemical oxygen demand (BOD5). Analysis of samples revealed a level of FCC that is above the permissible limit for both drinking water and of fresh vegetable irrigation water. In all, there is a pressing need to inform the public about the state of water bodies and the application of relevant laws regarding the proper treatment of sewage before it is discharged into surface water.