This study reports on a water quality assessment of the Water, Sanitation and Hygiene program implemented by the Swiss Agency for Development and Cooperation in the districts of Charsadda and Nowshera in Khyber Pakhtunkhwa, Pakistan, in the aftermath of the severe flood of 2010. During emergency operations, over 4,500 shallow wells were cleaned using the standard protocol suggested by the World Health Organisation. Bacteriological analysis and chemical-physical parameters such as temperature, conductivity, turbidity and pH were tested before and after cleaning. Four to five years after the emergency operation, in 2014–15, a set of 105 representative wells was analyzed again, considering the same parameters and looking for additional contaminants (pesticides, arsenic and fluoride). The post-flood well-cleaning campaign was effective in the immediate reduction of fecal contamination of water (from 85% to 20% as measured 7–30 days after cleaning), however in the following months/years the rate of fecal contamination rose again (up to 62% of all measured domestic wells, n = 105). Along with laboratory analysis data, this study investigated the source of contamination of shallow wells and identified human practices in several cases. This information was useful for the design of future SDC interventions in the WASH sector.