Because of the high subscription costs to the distribution network and water bills, access to running water for domestic use remains unaffordable to many inhabitants in cities and villages in the northern regions of Côte d’Ivoire. Thus, borehole and wells water is thus used as alternative to meet daily water needs, most often without a proper knowledge of the quality of such waters. This study aimed at evaluating the microbiological quality of borehole and well water in Ferkessédougou, one of the major cities in north Côte d’Ivoire. Chemical analyses were carried out on water sampled from 7 wells and 3 boreholes randomly selected across the study area. The results indicated that the average static level of the wells ranged from 0.5 m to 7.0 m. Water pHs were acidic to neutral and varied between 5.1 and 6.9. Faecal coliforms, Escherichia coli and intestinal enterococci were the main bacteria found in wells water, with proportions ranging between 2100 and 19000 CFU/100 ml, 120 and 5200 CFU/100 ml, and 30 and 240 CFU/100 ml, respectively. Only one borehole reported the presence of faecal coliforms (150 CFU/100 ml) and E. coli (15 CFU/100 ml). This faecal water pollution highlighted the poor sanitation conditions and unsuitability of water sourced from boreholes and wells to human consumption, indicating the need for adequate treatment of water prior to its use to avoid public health issues.