The Valley Elderberry Longhorn Beetle (“VELB,” Desmocerus californicus dimorphus) is a rare and cryptic species that is found on or near its host plant, blue elderberry (Sambucus mexicana), and is native to California’s Central Valley. Over the past 100 years, the riparian forests of Central California have shrunk by over 90%, resulting in highly fragmented, and often isolated, remaining VELB habitat patches. This has created the need for robust monitoring and demographic data to assess current and future threats to the species. In this study, we investigated VELB population viability and sensitivity to environmental and anthropogenic stochasticity across five major watersheds with known VELB populations. Additionally, we assessed how variability in three management scenarios influenced population persistence and extinction times, specifically the effects of increased habitat loss, more frequent drought and wildfires, and increased juvenile mortality due to invasive predators. We found that across all scenarios, the region-wide metapopulation was more robust to extinction than individual watersheds and that extinction probabilities were lower for larger watersheds than smaller ones. Specifically, we found that modest increases in the annual probability of drought or wildfires and juvenile mortality greatly reduced population persistence at all spatial scales, often leading to rapid watershed-level extinctions, while increases in habitat loss had moderate impacts. Contrary to previous thinking, we also found that increases in dispersal rates among watersheds had negligible effects on improving population viability. Our study highlights the vulnerability of VELB to further environmental and anthropogenic disturbance and emphasizes the importance of maintaining a healthy metapopulation structure with large tracts of suitable habitat for long-term VELB viability.