Current climate change exacerbates the environmental restrictions on temperate species inhabiting low latitude edges of their geographical ranges. We examined how temperature variations due to current and future climate change are likely to affect populations’ persistence of stream-dwelling brown trout Salmo trutta at the vulnerable southern periphery of its range. Analysis of 33 years of air temperature data (1975–2007) by time-series models indicated a significant upward trend and a pronounced shift in air temperature around 1986-1987. This warming is associated with an ongoing population decline of brown trout, most likely caused by a loss of suitable thermal habitat in lower latitudes since the 1980s. Population decrease may not be attributed to physical habitat modification or angler pressure, as carrying capacity remained stable and populations were not overexploited. We developed regional temperature models, which predicted that unsuitable thermal habitat for brown trout increased by 93% when comparing climate conditions between 1975–1986 and 1993–2004. Predictions from climate envelope models showed that current climate change may be rendering unsuitable 12% of suitable thermal habitat each decade, resulting in an overall population decrease in the lower reaches of around 6% per year. Furthermore, brown trout catches markedly decreased 20% per year. Projections of thermal habitat loss under the ecologically friendly B2 SRES scenario showed that brown trout may lose half of their current suitable habitat within the study area by 2040 and become almost extinct by 2100. In parallel to the upstream movement of brown trout thermal habitat, warm water species are increasing their relative abundance in salmonid waters. Empirical evidence was provided of how current climate change threatens some of the most healthy native brown trout populations in Southern Europe and how forthcoming climate change is expected to further decrease the conservation status of the species.