This study was conducted with the aim to monitor the suitability of the groundwater wells in Bugesera and Muhanga districts of Rwanda. As the quantity of water supplied by Rwandan Water and Sanitation Corporation ltd (WASAC) is not sufficient for the whole population in these districts, the people depend on groundwater as the main source of water. The microbial quality assessment made by this research on Bugesera district’s groundwater, obtained a number of total coliforms equaling to 132 MPN/100ml during dry season and 399 MPN/100ml during the rainy season with the fecal coliforms estimated to be 125 CFU/ml. In Muhanga district, total coliforms were estimated to be 125 MPN/100ml with the fecal coliforms estimated to be 115 CFU/ml. The microbial analysis results revealed the presence of Klebsiella, Escherichia coli, Shigella, Salmonella, M. morganii and Serratia spp in the groundwater wells of both districts confirming that groundwater wells are contaminated. Therefore, in order for this water to meet the standards of drinking water, it should be boiled or treated with chlorine before consumption and local authorities should be informed about the threats. Community participation and sensitization programs on how to obtain clean and safe water supply from groundwater need to be implemented by responsible stakeholders.