This research presents the results of a pilot system used for water treatment to be supplied to single-family or small housing nucleus at rural sector. The pilot system is constituted by an up-flow aerated filter with ceramic carrier, followed by a second down-flow filter of silica sand. The pilot plant was installed in a rural sector of the province of Loja, Ecuador, with the main purpose of monitoring the reduction in bacteria in the water for human consumption. Two natural clays from the area were tested. They were transformed into sphere-type ceramics, and then, they were placed in the pilot filters. These both natural clays are inorganic materials with high content of aluminosilicate clay minerals with favourable characteristics to achieve greater efficiency for the reduction in bacteria. The acclimatization time of 60days allowed to achieve optimum treatment efficiency performance until 90days of operation. The physicochemical parameters, namely temperature, pH, dissolved oxygen and total dissolved solids, were monitored throughout the experiments. Regarding microbiological parameters, up to 99% of total coliforms removal was reached for the clay called CF-CC and 79% for the other, called CF-CV. In addition, 100% of total coliforms and Escherichia Coli removal was reached for both clay systems. Social and economic viability of the proposed treatment is also analysed in the manuscript.