Current assessments of organismal vulnerability to global warming are focusing on physiological trait‐based indices that may allow biologically sounding estimates of heating risk at the local scale. However, intraspecific variability in both exposure and physiological performance may determine large heterogeneity in the distribution of heating risks through the overall species range compromising whole species risk assessments. We examine intra‐ and interspecific variability in two vulnerability indexes: warming tolerances (WT), or the extent that maximum temperatures (T
max) reaching upper thermal tolerances (CTmax); and thermal safety margin (TSM), or the magnitude that average environmental temperatures (T
mean) exceeding the selected or preferred temperatures (T
sel), in a subtropical warm amphibian tadpole community, at the Monte Desert ecoregion, Argentina. Tadpole populations breeds in temporary ponds and permanent streams that exhibit high thermal heterogeneity. Those populations and species living in hot water bodies, although exhibiting higher CTmax, have lower WT and are more prone to suffer acute heat impacts, thus confirming the prediction of higher thermal risk in ectotherms exposed to higher temperatures. However, these hot pond breeders, although living closer to their CTmax, also preferred high temperatures, showing higher TSMs and being actually exposed to a lower proportion of stressful temperatures than cool selecting populations. Both WT and TSM indexes have significant interpopulational variation. Thus, our findings suggest that attempts to build mechanistic models to forecast species vulnerability to heat stress due to climate change have to include physiological variation among populations.