The origin and distribution of microbial contamination in Oualidia lagoon were assessed using faecal coliform and streptococci bacteria. The lagoon is used for recreation, oyster farming and fishing. Samples were collected from 9 different sites and physicochemical and microbiological analyses which were performed monthly during 2 years (October 2003-October 2005). These samples were subjected to bacteriological analysis faecal coliform count and faecal streptococcal count. The physicochemical analysis of the water samples includes pH, temperature and specific conductance. The bacterial genera were identified on the basis of their morphological and physiological characteristics. The present study confirmed the presence of bacterial indicators of faecal origin at various stations in every stretch of Oualidia lagoon system. The samples collected from different sites of the lagoon showed wide variations in the counts of bacteria. The Bacterial population varied with seasonal variations in the water body. The Faecal coliform counts are increased during the summer months and lowered during the winter ones. The opposite happens of streptococci bacteria that are increased during the winter months and lowered during the summer ones depending on rainfall. Positive correlation was established between faecal coliform and streptococci bacteria. The results of bacteriological analysis of water revealed that the situation is alarming. The Bacteriological analysis of lagoon water indicated that water was polluted by faecal contaminants to the extent that it was unsuitable from the recreation point of view and hence needed thorough impoundment.