In the last two years, international AQUAPOT project has carried out the installation of three drinking water treatment plants based on ultrafiltration (UF), in rural areas of the Andean region of Ecuador without access to drinking water. In addition, the project has carried out an applied parallel investigation in the Naquera Research Centre (CIN) in Valencia that has by objective the anticipation to the problems that can arise in the operation of the drinking water facilities already installed, as a consequence of a non-rigorous cleaning protocol. For the investigation, analogous drinking water treatment plants to the ones installed in Ecuador have been used, working continuously in long-term operation assay and using as feed superficial water with a high microbiological contamination. Cleaning protocol was applied every 7 days using a cleaning solution an basic and acid agent followed by a disinfectant reagent. Results after 6 months of test, showed a progressive decrease of the permeate flow and presence of microbiological contamination. This work exposes main results and conclusions from real assays, and recommendations to achieve a correct operation of the UF plant.