<p>Just like calcium, magnesium, and iron, water is vital for life on our planet. Alarming evidence indicates that water is becoming scarce. In this critical situation, the management of hydric systems turns out to be a bottleneck. Established modes focus on regulation through laws and rulings. This paper offers a methodological contribution to improving the governance of River Basin Organizations (RBOs): a cybernetic model is introduced for the diagnosis and (re-)design of water governance, which is new in this context: the Viable System Model (VSM). This model embodies both a theory and a methodology, incorporating a heuristic cybernetic framework. The theory it provides is unique in its claim to specify the necessary and sufficient preconditions for the viability of any social system. It gives access to the deep structures that ensure the viability of social, and thereby socio-ecological and socio-technical systems. The VSM also provides a methodology that is highly beneficial in environmental, social, and economic terms. Using the VSM in the field of water governance is unorthodox and challenging. It has the potential to balance the need and supply of water, and even to reframe the system-in-focus, ensuring its viability and sustainability. The theoretical claim of the model is underpinned by an extensive case study from the Tocantins-Araguaia Hydrographic Region in Brazil—the largest hydrographic basin completely within Brazil. The insights gained from this account allow for cautious generalization and enable impactful applications.</p>