Climate change exposes benthic species populations in coastal ecosystems to a combination of different stressors (e.g. warming, acidification and eutrophication), threatening the sustainability of the ecological functions they provide. Thermal stress appears to be one of the strongest drivers impacting marine ecosystems, acting across a wide range of scales, from individual metabolic performances to geographic distribution of populations. Accounting for and integrating the response of species functional traits to thermal stress is therefore a necessary step in predicting how populations will respond to the warming expected in coming decades. Here, we developed an individual‐based population model using a mechanistic formulation of metabolic processes within the framework of the Dynamic Energy Budget theory. Through a large number of simulations, we assessed the sensitivity of population growth potential to thermal stress and food conditions based on a climate projection scenario (Representative Concentration Pathway; RCP8.5: no reduction of greenhouse gas emissions). We focused on three bivalve species with contrasting thermal tolerance ranges and distinct distribution ranges along 5000 km of coastline in the NE Atlantic: the Pacific oyster (Magallana gigas), and two mussel species: Mytilus edulis and Mytilus galloprovincialis. Our results suggest substantial and contrasting changes within species depending on local temperature and food concentration. Reproductive phenology appeared to be a core process driving the responses of the populations, and these patterns were closely related to species thermal tolerances. The non‐linear relationship we found between individual life‐history traits and response at the population level emphasizes the need to consider the interactions resulting from upscaling across different levels of biological organisation. These results underline the importance of a process‐based understanding of benthic population response to seawater warming, which will be necessary for forward planning of resource management and strategies for conservation and adaptation to environmental changes.