Introduction: The increase in waterborne diseases in certain remote areas of Benin led the study to conduct surveys on the different waters used by these inhabitants. Aims: This study is conducted to assess the probable risks related to the physicochemical and bacteriological quality of well water consumed by the population of the Tranza and Albarika neighborhoods. Place and Duration of Study: Water samples were collected from 20 wells (open and closed in Albarika and Tranza districts) in the Parakou commune and analyzed at the LaKReCA laboratory between April and July 2024. Methodology: A two-stage methodology was used to approach this study. Thus, a survey was conducted with the aim of determining the actual fraction of the population using well water as drinking water. The physicochemical and bacteriological parameters were determined according to standard normalization in order to assess water quality using Python software for the statistical study. Results: The results show that 26.66% of the inhabitants of the Tranza and Albarika districts are subscribers to SONEB against 20.01% who use well water as drinking water. In addition, the waters are colored (16.16±5.86 Pt/Co), cloudy (69±3.22 NTU), loaded (678.58±6.07 µS/cm), rich in magnesium (132.42±7.87mg/L), calcium (52.73±1.68mg/L), chlorine (88.23±1.96mg/L) and have high alkalinity contents (194.49±16.57mg/L). They are hard (185.09±5.09 mg/L) and can cause waterborne diseases depending on their total coliform (23 CFU) and E. coli (5 CFU) contents. The correlation between the parameters shows that a magnesium content equal to 67 mg/L leads to a high value of total coliform and calcium in well water. Conclusion: Ultimately, the origin of the pollution can be attributed to sanitation, household waste, the transfer of pollutants from surface layers, the conditions of drawing water and the structure of the wells. In the long term, the use of well water could constitute a significant health risk for the majority of the inhabitants of Tranza and Albarika in the city of Parakou.