The study measures the total economic value (TEV) of the flow of ecosystem services from the Cagayan de Oro (CDO) River Basin in Mindanao, Philippines. Estimates of the various components of TEV can serve as the basis and justification for the contributions that may be potentially collected from different economic sectors and social groups benefiting from the ecosystem’s services under a river basin-wide payment for environmental services (PES) scheme. Through PES, financial resources can be generated and used to reward local initiatives that restore and preserve the ecosystem. This approach has been identified as one strategic way to safeguard and enhance the continuing flow of environmental services from the river basin. Total benefits in the forms of stable supply of good-quality water, flood control, fishing and recreational value, and biodiversity are estimated to be about US$5.0–6.1 million per year.