Armed conflicts disrupt social, environmental and economic processes. This includes water resources management and the provision of water services, with numerous implications for human security and environmental sustainability. Such impacts go beyond direct, immediately visible effects and can have far-reaching, long-term consequences. However, the understanding of these indirect conflict impacts in different social and political contexts is still limited. In order to address this knowledge gap, we build on the social-ecological systems framework to differentiate between direct and indirect conflict impacts and to analyze their effects on the water system. We then apply the framework to map direct and indirect impacts of armed conflict on water resources management, using empirical data from eleven cases in Iraq, Syria, Palestine and Yemen. This allows us to identify pathways in which conflict impacts are propagated through the water system. The results show the central role of financial mechanisms in upholding water resources management throughout conflict and the importance of enforcing international humanitarian law on the protection of civilian infrastructure. They also highlight the value of system-based approaches in revealing cumulative effects that can reinforce conflict impacts within the system, and in identifying potential obstacles for coping strategies employed by local populations throughout the conflict.