For many years, the pesticides used in agriculture are responsible for environmental degradation, particularly noticeable in the areas of intensive agriculture, particularly through contamination of surface and ground water. Our study was conducted to isolate and identify the micro flora of water polluted by pesticides in an area with agricultural vocation (Ben MHidi) subject to the pesticide effect for several years. Isolated fungal strains were identified based on the morphology of their vegetative and reproductive apparatus. The micromycetes were obtained; they belong mainly to the genera Aspergillus, Penicillium and Trichoderma. Furthermore, most bacterial strains, characterized in this work is that of the genus Aeromonas, Pseudomonas that are widely represented in the study of the biodegradation of pesticides.