The increasing pressures of climate change and rapid population growth have intensified the interdependencies between water, energy, and food systems, particularly in Sub-Saharan Africa. This study examines how institutional fragmentation within the public sector constrains the governance of the Water–Energy–Food (WEF) nexus in the Democratic Republic of the Congo (DRC). Using a systematic literature review of 64 peer-review and reports combined with institutional mapping and expert validation, the analysis identifies the key actors, governance structures, and coordination challenges shaping WEF nexus management in DRC. The findings reveal a highly fragmented institutional landscape characterized by overlapping mandates, sectoral silos, and weak inter-ministerial coordination across water, energy, and food sectors. This fragmentation limits policy coherence, undermines integrated planning, and leads to inefficient resource allocation and conflicting sectoral priorities. Climate variability and demographic growth further exacerbate these challenges by increasing demand for resources while exposing structural weaknesses in administrative capacity and governance systems. The review also highlights that current governance institutions structural in DRC are not adapted to manage systemic interdependencies, resulting in trade-offs between sectors and limited ability to respond to complex, cross-sectoral challenges. In response, the paper proposes a conceptual framework for integrated WEF governance, emphasizing intersectoral coordination, collaborative governance, and multi-level policy coherence as key mechanisms to strengthen systemic resilience. The study argues that the primary constraint to WEF nexus management in the DRC is not resource scarcity, but governance fragmentation, and calls for context-specific institutional reforms to support integrated and adaptive resource governance.