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Hydrological alteration, which may be exacerbated by climate change, is known to facilitate aquatic species invasion. Altered hydrology, invasive species, and the additive effects of these stressors pose a threat to aquatic biodiversity. Understanding extinction risk in the context of these stressors is crucial for prioritizing conservation efforts. As case studies, three narrow-ranged endemic crayfish species of conservation concern (Faxonius marchandi, Faxonius roberti, and Cambarus hubbsi) in the Ozark Highlands of Arkansas and Missouri, USA, were used to examine the effects of invasive species and drought on crayfish population dynamics. The objectives of this study were to model the population dynamics of these imperilled species, assess how these populations may be affected under increased invasion effects and intensified drought, determine potential refuge effects, and examine the sensitivity of quasi-extinction to model parameters. ramas-metapop was used to construct stage-based demographic models. Terminal extinction risk, median time to quasi-extinction, and metapopulation occupancy were used to assess population viability under different scenarios. Cambarus hubbsi appears to be highly susceptible to decline if survival rates are reduced by simulated drought, as they have low reproductive potential and mature slowly. Models indicated that potential refuges allow F. roberti and C. hubbsi to persist, even when invasion and drought effects were extreme. Conversely, barriers to dispersal for F. marchandi led to reduced quasi-extinction times and the greatest extinction risk under most invasion scenarios. Quasi-extinction was most sensitive to changes in juvenile survival for all species examined, which indicates that improved estimates of stage-specific demographic parameters for crayfish will improve model predictions. An increased understanding of the mechanisms of displacement of native crayfish by invasive crayfish is needed for most crayfish species. Limiting the spread of invasive species, maintaining natural habitat and hydrological regimes, and gaining insight into life histories and demographic parameters will increase the ability to conserve endemic and imperilled crayfish.