Stream temperature controls important aspects of the riverine habitat, such as the rate of spawning or death of many fish species, or the concentration of numerous dissolved substances. In the current context of accelerating climate change, the future evolution of stream temperature is regarded as uncertain, particularly in the Alps. This uncertainty fostered the development of many prediction models, which are usually classified in two categories: mechanistic models and statistical models. Based on the numerical resolution of physical conservation laws, mechanistic models are generally considered to provide more reliable long-term estimates than regression models. However, despite their physical basis, these models are observed to differ quite significantly in some aspects of their implementation, notably (1) the routing of water in the river channel and (2) the estimation of the temperature of groundwater discharging into the stream. For each one of these two aspects, we considered several of the standard modeling approaches reported in the literature and implemented them in a new modular framework. The latter is based on the spatially-distributed snow model Alpine3D, which is essentially used in the framework to compute the amount of water infiltrating in the upper soil layer. Starting from there, different methods can be selected for the computation of the water and energy fluxes in the hillslopes and in the river network. We relied on this framework to compare the various methodologies for river channel routing and groundwater temperature modeling. We notably assessed the impact of each these approaches on the long-term stream temperature predictions of the model under a typical climate change scenario. The case study was conducted over a high Alpine catchment in Switzerland, whose hydrological and thermal regimes are expected to be markedly affected by climate change. The results show that the various modeling approaches lead to significant differences in the model predictions. It is also shown that the temperature of groundwater discharging into the stream has a marked impact on the modeled stream temperature at the catchment outlet. This supports the development of more accurate methodologies to estimate groundwater temperature in current hydrological models.