Abstract Integrating connectivity into systematic conservation planning is crucial to capture ecological processes and ensure long‐term conservation of biodiversity. Although advances have been made in structural and functional connectivity, most studies focus on single‐realm or single‐species approaches. This study applied the Marxan spatial prioritization tool to identify conservation priorities in the freshwater and marine realms under four scenarios, each applying different approaches to connectivity and threat propagation. Despite differences between scenarios, all met conservation objectives, and the planning units consistently selected between scenarios covered approximately 19% of the freshwater realm and 12% of the marine realm, highlighting priority conservation areas aligned with the Kunming‐Montreal Global Biodiversity Framework for 2030. The most effective approach integrated connectivity within and cross‐realm connectivity while taking into account propagated threats. When considering how threats from terrestrial upstream areas spread into connected freshwater and marine ecosystems, conservation areas were strategically placed in less threatened regions. This resulted in a more effective spatial configuration of the reserve system. Synthesis and applications . This study highlights the importance of integrating cross‐realm connectivity and threat propagation when designing new or expanding existing networks of conservation areas, such as the Natura 2000 European network of protected areas. These findings emphasize the need for multirealm planning that supports species persistence, protects transitional habitats and accounts for cross‐realm threats.
Vigo et al. (Wed,) studied this question.