Freshwater ecosystems are among the systems most threatened and impacted by anthropogenic activities, but there is still a lack of knowledge on how this multi-pressure environment impacts aquatic communities in situ. In Europe, nutrient enrichment and temperature increase due to global change were identified as the two main pressures on lakes. Therefore, we investigated how the interaction of these two pressures impacts the community structure of the two extreme components of lake food webs: phytoplankton and fish. We modelled the relationship between community components (abundance, composition, size) and environmental conditions, including these two pressures. Different patterns of response were highlighted. Four metrics responded to only one pressure and one metric to the additive effect of the two pressures. Two fish metrics (average body-size and biomass ratio between perch and roach) were impacted by the interaction of temperature and eutrophication, revealing that the effect of one pressure was dependent on the magnitude of the second pressure. From a management point of view, it appears necessary to consider the type and strength of the interactions between pressures when assessing the sensitivity of communities, otherwise their vulnerability (especially to global change) could be poorly estimated.