Waterborne pathogens present a significant threat to people living with the human immunodeficiency virus (PLWH). This study presents a randomized, controlled trial that evaluates whether a household-level ceramic water filter (CWF) intervention can improve drinking water quality and decrease days of diarrhea in PLWH in rural South Africa. Seventy-four participants were randomized in an intervention group with CWFs and a control group without filters. Participants in the CWF arm received CWFs impregnated with silver nanoparticles and associated safe-storage containers. Water and stool samples were collected at baseline and 12 months. Diarrhea incidence was self-reported weekly for 12 months. The average diarrhea rate in the control group was 0.064 days/week compared to 0.015 days/week in the intervention group (p < 0.001, Mann–Whitney). Median reduction of total coliform bacteria was 100% at enrollment and final collection. CWFs are an acceptable technology that can significantly improve the quality of household water and decrease days of diarrhea for PLWH in rural South Africa.