The country of Mexico is facing serious problems with water quality and supply for human use and consumption in rural communities, mainly due to topographic and isolation. In Mexico the average annual precipitation is 1,500 cubic kilometers of water, if 3% of that amount were used, 13 million Mexicans could be supplied with drinking water that they currently do not have access. Considering the limited infrastructure and management in rural communities, which do not receive services from the centralized systems of large cities, a modified pilot multi-stage filtration (MMSF) system was designed, developed, and evaluated for treating collected rainwater in three rural communities, Ajuchitlan and Villa Nicolas Zapata (Morelos State) and Xacxamayo (Puebla State). The efficiencies obtained in the treatment system were: colour and turbidity >93%. It is worth mentioning that the water obtained for human use and consumption complies with the Mexican Standard NOM-127-SSA1-1994.