In refugee and internally displaced person settlements, hygienic water handling and free residual chlorine (FRC) are crucial for protecting water against recontamination after distribution up to the household point-of-consumption. We conducted a secondary analysis of water quality and water handling data collected in refugee camps in South Sudan, Jordan, and Rwanda using statistical and process-based modeling to explore how water handling practices affect FRC decay and household FRC outcomes. The two practices that consistently produced a significant effect on FRC decay and household FRC were storing water in direct sunlight and transferring water between containers during household storage. Samples stored in direct sunlight had 0.22–0.31 mg/L lower household FRC and had FRC decay rates between 2 and 3.7 times higher than samples stored in the shade, and samples that were transferred between containers had 0.031–0.51 mg/L lower household FRC and decay rates 1.65–3 times higher than non-transferred samples in sites in which the effect was significant, suggesting that humanitarian responders should aim to provide additional water storage containers to prevent water transferring in households and encourage water-users not to store water in direct sunlight. By contrast, the effect of the three recommended hygienic water handling behaviors (clean, covered containers and drawing by tap or pouring) was mixed or inconclusive. These inconclusive results were likely due to imbalanced or unreliable approaches to gathering the data, and we recommend that hygienic water handling practices that mechanistically provide a physical barrier against recontamination should always be promoted in humanitarian settings.