Maroua, the capital of Far North Cameroon, is frequently affected by outbreaks of waterborne diseases. Waters stored through public clay pots are common in the city and provided voluntarily by individuals for drinking and ablution. Yet, such service through the clay pots and the stored water lacks management and surveillance. If contaminated, such water may pose infection and transmission risks of waterborne diseases among the population. The water quality of 95 randomly selected public clay pots was assessed through isolation and count of Total Coliforms (TCs) and Escherichia coli. Also analyzed was the bacteriological quality of the water source (borehole or tap) for comparison. For each clay pot, physical characteristics and management information were documented and potential sources of contamination were identified. Results showed that the concentration of TCs ranged from 0 CFU/100 mL in tap water to 160 CFU/100 mL in borehole water. The concentrations of E. coli varied from 0 CFU/100 mL in tap water to 2 CFU/100 mL in borehole water. Depending on the source of water supply and the neighborhood, the concentrations of total coliforms increased significantly in clay pots during water storage in most neighborhoods (P<0.05). Poor management and hygiene were responsible for water contamination.