Supplying safe drinking water in humanitarian emergencies is critical, and source water chlorination is a commonly implemented intervention to provide safe water. We evaluated three different source water chlorination programs (bucket, in-line, and piped water chlorination) in the ongoing humanitarian response in Cox’s Bazar refugee camps in Bangladesh. We used a mixed-methods research protocol including key informant interviews, water point observations, focus group discussions, household surveys, and water quality testing. The three evaluated programs were implemented at different response stages and required different levels of staffing, infrastructure, and community mobilization work. In the bucket chlorination program, highly contaminated open well water was chlorinated, in in-line and piped water chlorination programs, groundwater was treated. Overall, 71% of bucket, 36% of in-line, and 60% of piped water chlorination households had stored water that met free chlorine residual (FCR) criteria, respectively. Additionally, 71% of bucket, 86% of in-line, and 91% of piped water chlorination households had stored water that met Escherichia coli (E. coli) criteria (<10 E. coli CFU/100 mL). Regression results indicate presence of FCR, serving water by pouring, and higher source water pH were associated with meeting E. coli criteria. Our results highlight: no individual program fully met international standards as implemented, although each partially met standards; the importance of understanding beneficiary preferences and behavior change campaigns; and, the benefits and drawbacks of each source water chlorination program must be considered before implementation. Overall, we found appropriate source water chlorination program choice is a continuum, depending on humanitarian phase and context. Therefore, we recommend continuing context- and phase-appropriate source water chlorination programs, emphasizing consistent and acceptable chlorine dosage, implementing programmatic improvements, and incorporating user preferences to reduce microbial contamination and consequently the risk of waterborne diseases.