Southern pygmy perch, Nannoperca australis, is a small freshwater fish, whose range has declined in recent decades, particularly within New South Wales. The species is now listed as Endangered in both South Australia and New South Wales. Coppabella Creek, a small tributary of the Upper Murray River, is one of only three remaining locations where southern pygmy perch are know to exist within NSW. Over the past 10 years, like many regions of southern Australia, Coppabella Creek has experienced both ends of the extreme climatic spectrum, the driest period on record, followed by a succession of floods, including the highest on record. We followed the Coppabella Creek population through these climatic extremes and documented the impacts on their distribution and abundance. While there was significant drying of pools and losses of fish during the drought, the fish persisted in refuge sites. However, following flooding, there were significant declines in the both the abundance and distribution of the species. Abundance declined from 2375 individuals across 6 sites during the drought, to only 4 individuals at 2 sites post floods. During the drought, the distribution covered 28 of the 34 km of Coppabella Creek. Post flood, that distribution reduced to 7 km. We outline the management actions that were taken during these extreme events and discuss the implication of these actions on the future management of small threatened fish species populations.