This paper examines the hybrid institutional arrangements governing water security in post-conflict South Sudan. Based on a qualitative comparative case study of two sub-national states, it analyses how formal state agencies, customary authorities, and non-governmental organisations negotiate authority over water resources in practice. The findings reveal a landscape where customary systems, led by chiefs and water custodians, exercise primary de facto control over access and management, often operating in parallel to or in tension with a weak formal state apparatus. This hybridity manifests in both collaborative and conflictual interactions, directly shaping—and often entrenching—differentiated access along social and ethnic lines. Theoretically, the study advances the concept of hybrid governance by demonstrating how these emergent systems critically determine the delivery of an essential resource, moving analysis beyond a narrow focus on political or security institutions. It concludes that water governance serves as a microcosm of South Sudan’s contested statebuilding, where multiple sources of legitimacy coexist. For policymakers, the analysis underscores the necessity of engaging constructively with existing hybrid orders rather than imposing external, state-centric blueprints.