To compare both levels of water and air pollutants in Kigali city and Kitabi and benefits/disadvantages of the fuel types (gasoline, diesel and biodiesel) that are used in Rwanda, a parallel study on water and air pollution was conducted in Kigali city and Kitabi-Nyamagabe District during the January-July 2013 period. All vehicles entering Kigali City via Giticyinyoni, Nyacyonga, Gahanga and Rugende axes and the total number of motor vehicles in Rwanda were recorded. Carbon dioxide (CO2), carbon monoxide (CO), unburned hydrocarbons (HC) and opacity are the main emissions parameters measured at the Rwanda National Police Motor-vehicle Inspection Centre. The air quality parameters measured include HCl, NO2, NO3, SO2, H2S, TVOC, O3, CO and CO2 while quality of rain water harvested from the study sites was determined by measuring pH, conductivity, total dissolved solids, turbidity, biochemical oxygen demand, organic matter, sulfates, aluminum, copper, iron, manganese, cadmium, chromium, lead, sodium, and oils and grease. Kigali capital city suffers tremendous pressure of increasing population accompanied with the rapid increase in the number of vehicles which emit 526327.1 tons of CO2 year-1, 18405.5 tons of CO year-1 and 354967.0 m3 of unburned hydrocarbons year-1. Using 100% biodiesel reduced emission of CO by 50% and opacity by 76.9%, while using a 50% biodiesel blend or biodiesel-diesel mixture (B50) reduced CO by 35.2% and opacity which is strongly correlated with properties of particulate air pollutants by 71%. In Kitabi area, HCl, N02, TVOC, 03, CO2, NO3, SO2 and CO were reduced by 76.6%, 54.6%, 74.8%, 72.7%, 100%, 100% and 100% as compared with Kigali city respectively. Levels of acidic air pollutants (SO2 and NO2) are negatively correlated with rain water acidity (pH) levels (SO2: r = 0.787; NO2: r = 0.734) implying, therefore, that atmospheric deposition of strong acids or acidic pollutants lowers the water pH levels or increase water acidity. Reductions in atmospheric deposition of strong acids and other toxic pollutants may result in some improvements in the acid-base status of some water bodies which can lead to increased growth conditions for various organisms. The use of cleaner energies (i.e. biodiesel) therefore, may be a practical option of controlling emissions or managing air pollution causes. More detailed studies, however, are needed to determine the contribution (quantitative and qualitative) of each source of pollutants to both air and water pollution in Rwanda and identify other key emission control measures to be undertaken. Also efficiency of photosynthetic process of trees that are commonly planted in Kigali city needs urgent investigation.