Maintaining the functional integrity of ecosystems as climate pressures exceed natural rates of adaptation requires new knowledge and new approaches to governance and management. However, research into management interventions to assist regional ecosystem adaptation has generated both scientific and ethical debate. This paper reviews experience to date in order to identify the challenges and opportunities for assisted regional ecosystem adaptation and reflect on the implications for ongoing adaptation research. The review was informed by a database and structured analysis of some 450 reports, peer-reviewed manuscripts and books on participation theory and experience with novel technology development and assisted ecosystem adaptation. We identified five classes of challenges to adaptation research: 1) scientific conflicts and debates over the "facts", 2) social challenges, 3) governance challenges, 4) epistemic challenges, and 5) ontological conflicts. We argue that engagement strategies linked to the multiple objectives of adaptation research provide opportunities for ecosystem adaptation.