The groundwater of Saïs plain is the main drinking-water supply of Fez-Meknes region (Saïs basin) in Morocco. A large number of people living in this region depend on groundwater drawn from open dug wells for their daily water requirements. The main purpose of this study is to identify the major factors affecting groundwater quality by means an analysis of the microbial composition. The quality of 144 groundwater wells is evaluated in the Saïs plain according to microbiological measurements. The enumeration of total aerobic mesophilic flora, total coliforms, fecal coliforms, fecal streptococci, pseudomonas aeruginosa, salmonella and cholera vibrio were performed by the membrane filtration technique. The results showed that most of the water points studied are contaminated by Fecal coliforms, Total coliforms, Fecal streptococci, and Pseudomonas aeruginosa, their number in the waters of the analyzed wells exceeds the WHO recommendation and the Moroccan standards (0 CFU/ 100 ml). The bacterial load varies from one well to another with a slight seasonal variation. The quality of the water Saïs plain may be improved by cleaning of the groundwater sources, removal of organic matter from the water, the addition of a disinfectant or the boiling of drinking water before use. The study recommends regular monitoring of drinking water sources in this area for the presence of pathogenic bacteria.