Five thermal springs, twelve non-thermal springs, and two lake water samples from the northwestern part of Rwanda were studied to assess their chemical characteristics and infer the formation mechanism of the thermal waters. Multicomponent mineral equilibrium (MME) geothermometer calculations at Gisenyi prospects with the highest in situ measured temperature (73.1°C) showed the reservoir temperature of 90±6°C. The MME temperature estimates agreed well with Silica-based, K-Mg and Mg-Li geothermometers while the other cation geothermometers (Na-K, Na-K-Ca, Na-K-Ca-Mg, and Na-Li) results are unreliable. Most of the non-thermal springs are Ca-Mg-HCO₃ water-type while the thermal spring waters were majorly Na-HCO3. The δD composition varied from -16.6 to -5.9‰ and from -11.8 to -5.0‰, while the δ¹⁸O ranged from -4.17 to -3.5‰ and -4.32 to -2.7‰, for thermal and non-thermal springs, respectively. All isotopic ratios scattered around the meteoric water lines, thus indicating their similar meteoric origin. In addition, there was no observable δ¹⁸O positive shift speculating less extent of water-rock interactions while geogenic CO₂ ingress into the waters has been ascertained by both isotopic and chemical component ratios. We proposed a circulation mechanism of the thermal waters for the study area.