ABSTRACTMonitoring within an adaptive management framework provides important insights about system responses to management and information on which management actions to adjust to improve outcomes over time. We evaluated the range‐wide monitoring survey of the New England cottontail (Sylvilagus transitionalis) and assessed its ability to track changes in species’ population status over time using data gathered under the original protocol in 2016–2017 from 204 sites in 5 states (Connecticut, Maine, Massachusetts, New Hampshire, and New York, USA). We used occupancy analysis and structured decision making to evaluate 2 questions: 1) Does the monitoring survey provide the information needed to meet monitoring goals? and 2) What changes in the monitoring protocol, survey‐site selection, or field‐data collection are needed to better meet monitoring goals? A power analysis applied to data from the 2016–2017 survey indicated insufficient power (<0.80) to detect a large (0.50) change in occupancy, and either increasing the number of sites sampled, the number of occupied sites sampled, or both actions were needed to increase power and enable range‐wide survey objectives to be met. A revised study design was implemented in 2017–2018 that included sampling 146 of about 210 known occupied sites in 6 states (Connecticut, Maine, Massachusetts, New Hampshire, New York, and Rhode Island, USA) and provided sufficient power (0.81) to detect a small (0.30) change in occupancy. The revised study design revealed a 50% decline in the number of known occupied sites has occurred over the last decade. Our findings highlight the importance of study‐design considerations in monitoring protocols and the important role of structured decision‐making in making transparent, data‐informed, and defendable decisions when developing, evaluating, and revising monitoring plans for cryptic and rare species such as the New England cottontail. © 2020 The Wildlife Society.