Climate change is a poorly understood, emerging threat to many amphibian species. One of the ways climate change is likely to affect amphibians is through increased recruitment failure associated with more frequent climatic extremes. To understand the risk posed by this threat, we combined 13 years of annual monitoring and multi-scaled habitat modelling at the site (n = 60), pool (n = 105) and nest (n = 170) levels to investigate the decline of the endangered northern corroboree frog (Pseudophryne pengilleyi), during the most severe drought on record in southern Australia. We documented the local extinction of 42% of P. pengilleyi breeding sites during the climatic extreme. Using logistic regression we investigated habitat variables associated with extinction sites. We found that locally extinct sites now resemble historically absent sites, with fewer pools, less water, and drying-related tree invasion. Extended periods of limited water availability at extinction sites is likely to have restricted breeding, contributing to localised extinctions. Habitat variables recorded at the pool and nest level did not significantly influence P. pengilleyi presence/absence, indicating that site level wetness had an overriding effect. We anticipate that increasing climate variability is likely to disproportionately threaten seasonal pool-breeding amphibian species, exacerbating the global amphibian biodiversity crisis. However, our work with P. pengilleyi suggests there are a range of simple habitat manipulations that could help to ameliorate the impacts.