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Abstract Managers charged with recovering endangered species in regulated river segments often have limited flexibility to alter flow regimes and want estimates of the expected population benefits associated with both flow and nonflow management actions. Disentangling impacts on different life stages from concurrently applied actions is essential for determining the effectiveness of each action, but difficult without models that integrate multiple information sources. Here, we develop and fit an integrated population model for endangered Rio Grande Silvery Minnow (Hybognathus amarus) in the Middle Rio Grande, New Mexico. We integrate catch per unit effort monitoring data collected during 2002–2018 with population estimates, data collected during rescue of minnow from drying pools, habitat availability estimates, laboratory results, releases of hatchery reared minnow, and expert opinion. We use expert elicitation to develop a larval carrying capacity index as an informed proxy for the complex interactions among flow, habitat, and life history in this species. We evaluate the model using out‐of‐sample forecasts of 2019 and 2020, develop an algorithm to identify supplemental water releases that maximize benefits to the minnow, and quantify the effectiveness of various actions. Experts generally agreed on the duration and timing of flow requirements and disagreed regarding the importance of different magnitudes. The integrated model with the larval carrying capacity index outperformed two alternative models in forecasting catch in 2019 and 2020. The model estimates that minnow abundance varied by more than three orders of magnitude between 2002 and 2018 and that in a few years recruitment was limited by spawner abundance. Evaluation of the expected benefits of flow and nonflow management actions to fall population abundance across different years suggests that efficient addition of water to the base hydrograph is the most effective action in most, but not all years. Many actions are effective only under certain hydrologic and population conditions and the effectiveness of different actions varies in different sections of the study area. Widespread water extraction and river regulation combined with periodic drought and ongoing climate change may necessitate creative management of federally listed fish species in arid systems informed by thorough analyses of management effectiveness.