The Sawyer PointOne™ household hollow fiber membrane filter (PointOne) efficaciously removes microbiological indicators in the laboratory, and is increasingly considered for emergency response. To our knowledge, PointOne effectiveness in emergencies had not been evaluated. In South Sudan, 773 PointOnes were distributed. For 13 months after distribution, household surveys were completed quarterly, water quality testing was conducted monthly, and post-mortem analysis was completed at study midline to assess acceptability, effectiveness, and membrane fouling, respectively. Recipients found PointOnes acceptable, with high rates of demonstrated correct use (97–100%) and correct backflushing (96–100%). PointOnes effectively reduced thermotolerant coliforms for four months. When surface water use increased, effectiveness dropped, with 38% of filtrate samples contaminated. After backflushing filters with 0.2% chlorine solution, effectiveness improved; however, 5–38% of PointOne filtrate samples remained contaminated over subsequent months. Irreversible fouling was documented during post-mortem analysis. These results highlight that while PointOnes can improve household water quality within an emergency, PointOnes can foul within 4–6 months of use, depending on influent water quality. It is recommended that future PointOne distributions include continuous monitoring and an appropriate cleaning regime, based on influent water quality, to ensure continued performance. Further research on source water quality impacts on PointOne performance is recommended.