We provide an assessment of thermal habitat vulnerability in the upper Shavers Fork sub-watershed, West Virginia, which currently supports a brook trout metapopulation. We quantified variability in observed (2001–2015) summer stream temperatures (TS) across 23 (9 tributary, 14 main-stem) reaches. We developed a mixed effects model (R2=0.93; RMSE=0.76oC) to predict mean daily TS from air temperature (TA) and discharge (Q) and coupled this model with a hydrologic model to predict future (2016–2100) TS. Observed TS exceeded the 21oC physiological threshold in all but one main-stem site, while 3 sites exceeded 63- (21.0oC) and 7-day (23.3oC) thermal limits. TS was predicted to increase across main-stem (0.2–1.2oC) and tributary (0.3–1.2oC) sites. From 2091–2100, the number of days with TS> 21oC increased across main-stem sites (0-13 days); however, no site exceeded 61- or 7-day thermal limits. During the 10 years with the greatest ∆TS, >5 sites exceeded thermal limits. Years with large ∆TS were characterized by low Q relative to increased TA. Reaches below major tributaries never exceeded thermal limits. Persistence of thermal refugia would enable persistence of meso-scale metapopulation structure. However, this will only be possible if projected increases in Q are realized and offset increased TA.