Climate change, population growth, and declining federal budgets are threatening the health of ecosystems, and the services they provide. Under these changing conditions, managing landscapes and resources assumes new and unprecedented challenges. Adaptive management has been identified as a natural resource management approach that allows practitioners to incorporate change and uncertainty into decision-making through an iterative process that involves long-term monitoring and continued review and adjustment of management actions. However, the success of these efforts in watershed health relies on the collective and sustained monitoring of indicators, which is seldom studied. The purpose of this analysis is to examine (1) the practical challenge of choosing a list of indicators for long-term monitoring, (2) the negotiation process among stakeholders around the selection and interpretation of indicators, and (3) the communication tools that can be used to convey the assessment’s results and findings. To do this, we analyze our ongoing work in the Cienega Watershed in southern Arizona. Our analysis shows that the selective use of indicators, regular assessment and review, and establishment of partnerships among stakeholders are all important elements in establishing effective adaptive management efforts. The selection of indicators and data sources is a moving target that requires regular consensus and review among stakeholders. The assessment itself is also a powerful engagement tool with the public at large, providing legitimacy and support to land management decision-making. Here, we outline some lessons learned that can be transferred to other cases and identify potential barriers for engagement, decision-making, and project success.