Diadromous fish species have a complex life cycle during which they migrate between marine and freshwater habitats. They experience multiple human-induced pressures in both environments, likely exacerbated by climate change, leading to dramatic population declines across their distribution ranges. Currently Species Distribution Models (SDMs) have been applied separately in both their continental and marine habitats to improve our understanding of their lifecycles and help with species management. Integrating the freshwater-sea continuum into the decisions would now be a step further in improving their management. With this objective, we developed a decision tree that links marine and freshwater SDM outputs with current observations of population functionality and suggested management guidance options for the viability of these species. Potential effects of climate change were included through future SDM projections to guide integrative and long-term management. Several criteria were proposed to assess the SDM validity considering the main sources of SDM uncertainties and local expert knowledge on habitat and population status. The framework was applied to approximately one hundred catchments from southern Portugal to southern Scandinavia for four diadromous species. At the European level, management guidance options differed between the two anadromous and two catadromous species. Platichthys flesus and Chelon ramada European populations seemed in better state than those of Alosa alosa and A. fallax. Finally, with the help of national diadromous species experts, we focused on four catchments distributed along the European latitudinal gradient to test the proposed methodology and demonstrate local management challenges in terms of freshwater-sea continuity.