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For freshwater systems, climate change-induced alterations to drought regimes are a considerable threat to already threatened species. This is particularly poignant for kowaro (or Canterbury mudfish, Neochanna burrowsius), a critically endangered fish largely restricted to drying-prone waterways on the Canterbury Plains, New Zealand. By comparing three catchment-wide surveys (2007, 2010, 2015) within the Waianiwaniwa Valley, we assessed the scale and magnitude of population change induced by 2 years of consecutive drought (2014-15), when compared to surveys during wetter conditions (2007, 2010). The droughts triggered a catchment-wide switch from adult-dominated populations to populations comprised of juveniles indicated by a significant reduction in median size (similar to 95 mm during the wet to similar to 60 mm after drought). In comparison, population abundances were highly variable, indicated by no significant change in catch-per-unit-effort. The large variation in catch rates and connection of median size to reproductive potential mean median size will be useful to measure in monitoring to infer potential changes to population resilience, particularly during extreme events. Furthermore, because N. burrowsius could be regarded as extremophile fish, already restricted to harsh habitats, they are likely to become increasingly threatened by climate change. Thus, tools that allow for insightful comparisons between populations, such as a population resilience framework based on both abundance and body size distribution, will be increasingly important for pragmatic decision-making for targeted conservation measures.