Identifying mediator factors linking climate changes and ecological processes in pelagic food-webs is a major challenge in ecology and resources management. Here, we have investigated how climate variability affects marine and limnic ecosystems. We used a downscaling and time-series modelling approach in which we analyzed different spatial scales of climate for a period spanned from 1950 to 2005 in two location areas: the Ligurian Sea in the Northwestern Mediterranean and the Lake Geneva in the European Alps. Results provide substantial evidence of the Atlantic climate control on the long-term changes in pelagic trophic levels, from primary producers to fish, in the two ecosystems for the past three decades, although Lake Geneva was further affected by nutrient enrichment related to anthropogenic stress. Through direct effects on pelagic organisms, climate warming affects fecundity and developmental time, but also alters ecological interactions (i.e. predation and competition) that ultimately allowed to reorganisations in the investigated pelagic ecosystems. The results further show that climate forcing varies seasonally leading to different roots of large-scale climate forcing on the target sites: while the North Atlantic climate dominated the winter-spring period, the Subtropical Atlantic climate strongly affects the summer-autumn period. The cascade of interactions we identified, from large-scale climate to ecological processes, allow suggesting empirical models to explain how climate interacts with these pelagic ecosystems. These findings deserve attention to be considered in the assessment and modelling of pelagic food-webs and biogeochemical fluxes in climate change scenarios. They also draw attention to synchronous regime shifts in the investigated ecosystems that have occurred simultaneously with ecological regime changes documented in the Northern Hemisphere, and thus raise the question of plausible region-wide environmental shifts linked to climatic changes.