This study discusses some insights for adaptive aquatic ecosystem management, based on evidence of upstream-downstream financial partnerships on watershed scales, or watershed-based Payments for Ecosystem Services (PES) programs. Socioeconomic and watershed information on 13 advanced PES programs being implemented in 13 developing countries was collected and synthesized to analyze their partnership structures. Structured by the distributions of downstream payers and upstream payees within specific legislative tiers and hydrological orders, the PES partnerships revealed three important features with broad implications for aquatic ecosystem management: (1) institutional incentives for water resources, (2) participation units within the watersheds, and (3) organizing scopes for aquatic ecosystem management. In particular, as a reflection of organizing scopes, landscape entrepreneurship, or development of new organizations on the landscape, suggested two visions for adaptive aquatic ecosystem management: (1) connective lifestyles of individual stakeholders, with a transformation from benefiting from ecosystem services to providing conservation services, and (2) compatible technological innovations among organizational stakeholders, with a transformation from supplying latent and disconnected organizing services to strengthening systematic and accountable organizing services. This study is intended to provide a socioeconomic perspective to bridge the domains of water resources management, watershed management, and aquatic ecosystem management, in order to substantially promote diverse scales of stakeholder behavioral adaptations for the common mission of sustainable development in our societies.