Climate change exerts a significant influence on lake ecosystems by altering stratification and thermal dynamics. These changes are commonly quantified using climate model projections to assess future conditions. However, climate model simulations generally have a daily temporal resolution, which is inadequate for resolving the fast, sub-daily processes governing shallow lakes. Consequently, long-term impacts of climate change on shallow lakes remain underrepresented in literature. This study presents a modeling workflow for simulating and quantifying future climatic conditions in shallow environments, where sub-daily resolution is necessary. The proposed workflow comprises a weather generator for the temporal downscaling meteorological forcing, as well as a physics-based one-dimensional model for simulating lake thermal dynamics. The workflow is applied to Lake Blaton, a large polymictic lake, to assess the effects of the projected climatic changes on the lake through the end of the century. Changes are analyzed as a function of time and water depth, under the RCP4.5 and RCP8.5 climate scenarios, using an ensemble of 14 climate model simulations. Our findings indicate that stratification is likely to intensify throughout the century, in a complex interplay with water depth, in which mutually enhancing effects are accompanied by progressive dampening. The number and duration of stratified events show a slight increase, which does not reflect the magnitude of the projected intensification in stratification, suggesting that wind forcing remains a dominant factor in regulating stratification dynamics. Lastly, the evaluation of lake heatwaves using a temporally varying baseline indicates no significant changes in their characteristics.