In semi-arid regions, groundwater-dependent ecosystems rely on stable hydro-thermal regimes where refugia have supported aquatic biota for millennia. In karst systems, springs provide consistent flows and stenothermal conditions that buffer extremes. Our objective was to assess the impacts of spring discharge on instream temperatures, using the pristine Devils River in Texas as a case study, where climate change and groundwater development threaten to reduce spring flows and aquatic habitats of protected species (Devils River minnow and Texas hornshell mussel). Instream temperatures and discharge were monitored for three years above and below the Finegan Spring complex. These time series were extended back 30 years using temperature data from North American Land Data Assimilation System (NLDAS) land surface models. Monitoring data revealed that springs contributed similar to 40% of total river discharge. Spring temperatures were consistently 22.6 +/- 0.3 degrees C providing thermal refugia to 200 m of river-cooling the streamflow in summer and warming it in winter, with a noted stratification overturning each winter. High correlations between NLDAS air and soil temperatures and instream temperatures allowed the water temperature record to be extended over 30 years. While air and soil temperatures increased 0.35 degrees C and 0.30 degrees C per decade, spring inputs from karst aquifer buffer downstream temperature increases to 0.12 degrees C per decade. Furthermore, spring discharge reduced the duration of extreme thermal habitat thresholds by 50-70%. A similar approach could be applied to other groundwater dependent ecosystems with sparse temperature data. The results underscore the importance of spring discharge in maintaining heterogeneous aquatic habitats in karst terrain.