The question of how the complexity of water governance may be understood beyond a heuristic concept remains unanswered. In this paper, we propose a Water Governance Complexity Framework to address the complexity of water governance. Through a literature review, rapid surveys, and 79 semi-structured interviews, we propose how this framework may be operationalized using different proxies and by applying it to the case of the water supply system for domestic use in Oaxaca, Mexico. In places such as the rural communities of Oaxaca, where the state plays a partially absent role in the water supply, we found legal pluralism and diverse formal and informal stakeholders in a multi-level structure. At the local level, four modes of governance were identified, resulting from seven institutional change trajectories. These trajectories result from linear (alignment) and non-linear (resistance and adaptation) interactions between local, state, and national institutions over different periods. We provide a pragmatic framework to understand complexity through the organization and historical configurations of water governance that may be applied globally, providing a necessary starting point and solid foundation for the creation of new water policies and law reforms or transitions to the polycentric governance model to ensure the human right to water and sanitation.