Marine organisms are currently experiencing an unprecedented rate of climatic warming, which affects their biogeography and threatens marine ecosystem integrity. To understand how benthic species will respond to ongoing seawater warming, we assessed the relative importance of processes acting at different scales using an individual-based modelling approach. Our model integrates: (1) at the individual scale, interactions between the environment, metabolism and ontogenic transitions; (2) at the habitat scale, competition for space at settlement and mortality; and (3) at the regional scale, larval dispersal and connectivity between habitats. We focused on a coastal area in the North-East Atlantic that has experienced a significant seawater warming trend over recent decades. We built and ran a population dynamics model for the blue mussel (Mytilus edulis) in this area, which is a known biogeographic boundary zone. We then compared the response for a reference scenario and a RCP8.5 temperature projection for 2100. We found that (1) increase in seawater temperature would result in a decrease in average biomass associated with a change in recruitment phenology; (2) response to seawater warming is not spatially homogeneous, showing the importance of processes at the habitat scale; (3) connectivity clearly limits the consequences of warming compared with other regulation processes; and (4) larval supply does not seem to be a limiting factor regulating population biomass. The use of such generic models would therefore be very valuable for guiding and optimizing research efforts and supporting the implementation of management and conservation measures.