Anthropogenic pressures have resulted in declines in diadromous fish. Many diadromous fish which were commercially important are now threatened and protected. Little is known about their marine life history phases, and no observation-based Species Distribution Model exists for this group of species at sea. Yet, fisheries dependent and independent data could provide new insights into the distribution of diadromous fish at sea. We collated a database of 168 904 hauls from fisheries observer bycatch data and scientific fisheries surveys, from eastern Atlantic and Mediterranean waters. The distribution of eleven rare and data-poor diadromous fish (shads, lampreys, salmonids, the European eel, the thinlip mullet, smelt and the European flounder) were modelled. A Bayesian site occupancy model, that incorporates imperfect detection to account for repeat detections and non-detections, the non-random nature of fishing gear type and spatial autocorrelation was used. From the model outputs, we explored bycatch risk and the role of MPAs, required under the Marine Strategy Framework Directive and Habitat Directive and assessed. Diadromous fish were observed within relatively shallow coastal areas. Species specific gear bycatch trends were observed. Core distribution areas corresponded to their known water basin presence, indicating connectivity with their freshwater habitats. Numerous Habitat Directive Marine Protected Areas were found to be of relevance. Given the coastal distribution of these species, they are exposed to higher anthropogenic pressures from both terrestrial and marine environments. Risk of bycatch at sea for most species appears to be low. Nonetheless, for threatened individuals, even a small amount of bycatch may impact their populations, especially since misreporting is likely to be high. Differences in catchability between gears highlight potential benefits of limiting access of certain gears within protected areas to reduce bycatch.