Mixed agroforestry systems offer opportunities to simultaneously meet the water, food, energy and income needs of densely populated rural and peri-urban areas in Indonesia. Water flows out of upland areas provide multiple ecosystem services to downstream areas that can be part of performance-based rewards, payments or co-investment in environmental stewardship. Metrics for measuring performance and negotiating accountability need to cover river (blue), soil + vegetation (green), recycled (gray) and atmospheric (rainbow) water in relation to specific stages in the water cycle and associated services. A typology of services and prototype payment mechanisms were derived from action research in Indonesia and elsewhere in Asia by the Rewarding Upland Poor for Environmental Services (RUPES) project. The ecological metrics of landscape performance can be combined with measures of human capacity to assess and support the resilience of social-ecological systems under climate change.