Identifying which factors influence household water management can help policy makers target interventions to improve drinking water quality for communities that may not receive adequate water quality at the tap. We assessed which perceptional and socio-demographic factors are associated with household drinking water management strategies in rural Puerto Rico. Specifically, we examined which factors were associated with household decisions to boil or filter tap water before drinking, or to obtain drinking water from multiple sources. We find that households differ in their management strategies depending on the institution that distributes water (i.e. government PRASA vs community-managed non-PRASA), perceptions of institutional efficacy, and perceptions of water quality. Specifically, households in PRASA communities are more likely to boil and filter their tap water due to perceptions of low water quality. Households in non-PRASA communities are more likely to procure water from multiple sources due to perceptions of institutional inefficacy. Based on informal discussions with community members, we suggest that water quality may be improved if PRASA systems improve the taste and odor of tap water, possibly by allowing for dechlorination prior to distribution, and if non-PRASA systems reduce the turbidity of water at the tap, possibly by increasing the degree of chlorination and filtering prior to distribution. Future studies should examine objective water quality standards to identify whether current management strategies are effective at improving water quality prior to consumption.