We evaluated the ability of UNICEF-designed pot-chlorinators to achieve recommended free residual chlorine (FRC) levels in well water in Bissau, Guinea-Bissau, during a cholera outbreak. Thirty wells were randomly selected from six neighbourhoods. Pot-chlorinators – perforated plastic bottles filled with gravel, sand and calcium hypochlorite granules – were placed in each well. FRC was measured before and 24, 48 and 72 h after placement and compared with World Health Organization (WHO)-recommended levels of ≥1 mg L−1 for well water during cholera outbreaks and 0.2–5 mg L−1 in non-outbreak settings. Presence of well covers, distance from wells to latrines, and rainfall were noted. Complete post-chlorination data were collected from 26 wells. At baseline, no wells had FRC >0.09 mg L−1. At 24, 48 and 72 h post-chlorination, 4 (15%), 1 (4%) and 0 wells had FRC ≥1 mg L−1 and 16 (62%), 4 (15%) and 1 (4%) wells had FRC between 0.2 and 5 mg L−1, respectively. Several families reported discontinuing household water chlorination after wells were treated with pot-chlorinators. Pot-chlorinators failed to achieve WHO-recommended FRC levels in well water during a cholera outbreak, and conveyed a false sense of security to local residents. Pot-chlorination should be discouraged and alternative approaches to well-water disinfection promoted.