The drinking water supply in Yaounde, Cameroon, often fails to meet demand and this leads many people to seek water from springs and wells the microbiological quality of which is unknown. We carried out a microbiological survey of five spring water points and ten wells. The fifteen study sites were located in various residential districts and were selected according to geographical location and number of users. Microorganisms were isolated on specific culture media using the membrane filter technique. We found that these water supplies contained many types of bacteria including Pseudomonas aeruginosa, Aeromonas hydrophila and indicators of fecal contamination. Maximum annual concentrations differed at the various sites and over time, from 750 to 98,000 CFU/l for P. aeruginosa, 40 to 78,000 CFU/l for A. hydrophila and 300 to 58,000 CFU/l for fecal indicator bacteria. The density of fecal bacteria was strongly correlated (p < 0.01) with those of P. aeruginosa in spring water and A. hydrophila in well water. The degree of correlation between microbial concentrations differed between sites. The source of fecal contamination differed between sites and was animal, human or both. The densities of bacteria recorded were high. Therefore, consumers of water drawn from these sources are at short-term risk of contracting waterborne diseases.