Introduction: water is used predominantly in food manufacturing process. Northern morocco agro-food industries use different sources of water, but public water and wells water are the main sources of water used. This water can be the main source of possible food contaminations and alterations. This study aims is to assess the bacteriological quality of water used in the agro-food industries in the Northern region of Morocco, to identify the different types of germs responsible for the pollution of these waters and to establish the main causes of this pollution. Methods: water samples taken from taps or wells were analyzed to detect pollution indicator germs (total coliform (TC), fecal coliform (PC), intestinal enterococci (E), revivable microorganisms (RM), sulphite-reducing anaerobes) and pathogens (Salmonella, Staphylococci, Pseudomonas aeruginosa). The enumeration of the bacteria was performed by filtration technique and incorporation obtained through supercooled solid state. Results: the results showed that public-supply waters were of satisfactory bacteriological quality while 40% of the wells water was non-compliant with water quality standards due to the presence of TC, FC, E and RM pollution indicators. In contrast, pathogens, particularly Salmonellae, were absent in all the wells water analyzed. Conclusion: well water pollution was generally due to failure to meet hygienic requirements for water pumping. Bacteriological quality of these wells water could be improved by adequate protection.