Marine organisms are currently, and will continue to be, exposed to the simultaneous effects of multiple environmental changes. Plankton organisms form the base of pelagic marine food webs and are particularly sensitive to ecosystem changes. Thus, warming, acidification, and changes in dissolved nutrient concentrations have the potential to alter these assemblages, with consequences for the entire ecosystem. Despite the growing number of studies addressing the potential influence of multiple drivers on plankton, global change may also cause less obvious alterations to the networks of interactions among species. Using inverse analyses applied to data collected during a mesocosm experiment, we aimed to compare the ecological functioning of coastal plankton assemblages and the interactions within their food web under different global change scenarios. The experimental treatments were based on the RCP 6.0 and 8.5 scenarios developed by the IPCC, which were extended (ERCP) to integrate the future predicted changes in coastal water nutrient concentrations. Overall, we identified that the functioning of the plankton food web was rather similar in the Ambient and ERCP 6.0 scenarios, but substantially altered in the ERCP 8.5 scenario. Using food web modelling and ecological network analysis, we identified that global change strengthens the microbial loop, with a decrease of energy transfer efficiency to higher trophic levels. Microzooplankton responded as well by an increased degree of herbivory in their diet and represented, compared to mesozooplankton, by far the main top-down pressure on primary producers. We also observed that the organisation of the food web and its capacity to recycle carbon was higher under the ERCP 8.5 scenario, but flow diversity and carbon path length were significantly reduced, illustrating an increased food web stability at the expense of diversity. Here, we provide evidence that if global change goes beyond the ERCP 6.0 scenario, coastal ecosystem functioning will be subjected to dramatic changes.