Amphibians and fishes play a central role in shaping the structure and function of freshwater environments. These organisms have a limited capacity to disperse across different habitats and the thermal buffer offered by freshwater systems is small. Understanding determinants and patterns of their physiological sensitivity across life history is, therefore, imperative to predicting the impacts of climate change in freshwater systems. Based on a systematic literature review including 345 studies with 998 estimates on 96 amphibian and 93 freshwater fish species, we conducted a meta-analysis to explore phylogenetic, ontogenetic, and biogeographic (i.e. thermal adaptation) patterns in upper thermal tolerance (CTmax) and thermal acclimation capacity (Acclimation Response Ratio, ARR) as well as the influence of the methodology used to assess these thermal traits using a conditional inference tree analysis. We found CTmaxand ARR differed between taxa, pre- and post-metamorphic life stages as well as with thermal adaptation. The ARR of freshwater fishes exceeded that of amphibians by more than twice across life stages. In amphibians, CTmaxdecreased throughout early development, with juveniles exhibiting the lowest heat tolerance, potentially representing a life history bottleneck if other strategies to reach thermal refugia, e.g. through behavioral thermoregulation, would also be constrained. In contrast to the broader literature, CTmaxwas not generally higher in low latitude populations but also varied with ontogeny, emphasizing the importance of assessing life stage- specific sensitivity to thermal stress. Importantly, the application of different methods (e.g. acclimation duration, ramping rates) changed life stage, phylogeny, and thermal adaptation patterns in CTmaxand ARR. Our analyses highlight biases and data limitations with respect to coverage in taxonomy, biogeographic distribution of species, life stage, and study design. We propose methods to improve robustness and comparability of thermal sensitivity knowledge needed to adopt interventions to safeguard freshwater biodiversity in a future climate.