Monitoring and reporting of water resources is fundamental for developing long term plans for its conservation, protection and efficient use. Water Accounting Plus (WA+) is a comprehensive water accounting framework that provides coherent water resources information for all relevant stakeholders using primarily remotely sensed and open access data. WA+ reports on the current state of a river basin, its current and future challenges, and identifies improvement opportunities. The WA+ framework was applied to the eight main river basins of Mindanao, the second-largest island of the Philippines, for the period 2014–2019. The results showed that, though Mindanao Island has abundant water resources, there is considerable monthly and yearly variability in the precipitation it receives. The availability of water in the basins shows both temporal and spatial variability driven primarily by the amount of precipitation. The monthly variability is more pronounced than the annual variability while spatially, the northern basins have more available water than the basins located in central and southern parts. All the basins generate surplus water but only 3% of this water is currently managed. To satisfy the increasing demand of water during dry years and months, strategies focusing on increasing water productivity and storage capacity are recommended to ensure a resilient development of the water resources and to mitigate future impact of climate change.