Headwater stream ecosystems are vulnerable to numerous threats associated with climate and land use change. In the northeastern US, many headwater stream species (e.g., brook trout and stream salamanders) are of special conservation concern and may be vulnerable to climate change influences, such as changes in stream temperature and streamflow. Federal land management agencies (e.g., US Fish and Wildlife Service, National Park Service, USDA Forest Service, Bureau of Land Management and Department of Defense) are required to adopt policies that respond to climate change and may have longer-term institutional support to enforce such policies compared to state, local, non-governmental, or private land managers. However, federal agencies largely make management decisions in regards to headwater stream ecosystems independently. This fragmentation of management resources and responsibilities across the landscape may significantly impede the efficiency and effectiveness of conservation actions, and higher degrees of collaboration may be required to achieve conservation goals. This project seeks to provide an example of cooperative landscape decision-making to address the conservation of headwater stream ecosystems. We identified shared and contrasting objectives of each federal agency and potential collaboration opportunities that may increase efficient and effective management of headwater stream ecosystems in two northeastern US watersheds. These workshops provided useful insights into the adaptive capacity of federal institutions to address threats to headwater stream ecosystems. Our ultimate goal is to provide a decision-making framework and analysis that addresses large-scale conservation threats across multiple stakeholders, as a demonstration of cooperative landscape conservation for aquatic ecosystems. Additionally, we aim to provide new scientific knowledge and a regional perspective to resource managers to help inform local management decisions.