Populations can be granted conservation status because they harbour a set of unique traits, evolutionary histories, or ecological roles. Such populations are often isolated and specialized and, as such, can be particularly vulnerable to environmental disturbances. Even if distinct populations survive and adapt to severe disturbances, they could show changes in the very traits that made them distinct in the first place. Here, we leverage a natural “experiment” involving an unarmoured population of threespine stickleback (Gasterosteus aculeatus) in Rouge Lake (Haida Gwaii, BC) – a population listed as Special Concern under the Canadian Species at Risk Act. In 2015, Rouge Lake nearly dried up during a severe drought event; yet the stickleback population appeared to have fully recovered its abundance in subsequent years. Using phenotypic measurements, we assessed the extent to which evolution in this population was impacted by the drought. We document important shifts in several phenotypic traits, with the largest occurring in precisely the trait that made the population distinct and prompted its original conservation designation. Specifically, fish with no lateral plates (i.e., “unarmoured”) made up 51 % of the population before the drought, but only 13 % after the drought. This shift held (13-16 % unarmoured) over the four years of our post-drought monitoring. Field observations support a strong demographic bottleneck, which we suggest might have been coupled with a shift in the selective regime. These findings underscore how populations of conservation concern are not only at risk of extinction; they are also at risk of losing the characteristics that make them unique. These dynamics highlight the need for policies to consider a population’s evolutionary potential and develop more flexible approaches than simply considering single-timepoint assessments of diversity.