Conflicts of interest due to cultural, political, and social oversights have threatened effective and efficient corporate water governance in Nigeria. This has affected the inclusive participation of stakeholders, policy makers and the relevant agencies of the water resources management, thus hampering good water governance. Assessing the water governance impacts based on frameworks proposed for effective, efficient and inclusive governance was aimed. Information contributing to the governance input was highlighted by analyzing hydrological units that characterized Nigerian watersheds. Toxicological index (Ti) values were presented as a practical guideline to assessing water policy outcomes. The (Ti) ≥ 1.0 dominated; signifying the water resources exposed to toxic environments. High pollutant loads associated with public health deterioration across Nigeria are considered as impacts indicating lagged water governance. While the lagged governance output manifested in some diseases relating to deficient access to potable water supply/poor sanitation services like Blue baby syndrome, Renal/liver/lung diseases and blood cancer, the outcome showed an absence of health and social wellbeing. These indicators demonstrate the need for incorporating Organization for Economic Co-operation and Development (OECD) Principles on Water Governance in the Nigerian water governance system. Notably, flexibility across all governance levels can enable shared responsibility to balance economic activities with the ecological wellbeing.