Multi‐year and multi‐site demographic data for rare plants allow researchers to observe threats and project population growth rates and thus long‐term persistence of the species, generating knowledge, which allows for effective conservation planning. Demographic studies across more than a decade are extremely rare but allow for the effects of threats to be observed and assessed within the context of interannual environmental variation. We collected demographic data on the Threatened plant Cirsium pitcheri in two sites from 2011–2022. These sites were chosen because one exhibited the presence of non‐native seed predators while the other did not, and we hypothesized that we would see declines and potentially extinction of the population threatened by predation. Over the course of our study, we observed additional threats, such as human trampling and high lake levels, which led to significant erosion, sand burial, and storm damage to plants. We find high interannual variation in vital rates and population growth rates for both populations, which mask the overall effects of predation. We observed dramatic declines in plant survivorship and population growth rates in both sites in the years with high lake levels. We conclude that high lake levels, which are expected to become more frequent with climate change, pose a significant threat to all near‐shore populations of C. pitcheri.