Abstract
Fjords are deep-water estuaries that support a wide range of marine habitats for pelagic fish. Yet, knowledge gaps in fish distribution and habitat use limit the implementation of efficient marine conservation strategies within fjords. Using five British Columbia fjords as a case study, we demonstrated that eDNA metabarcoding combined with species traits can enhance the detection and monitoring of conservation priority species (CPS) within systematic conservation planning frameworks. Spatiotemporal eDNA patterns confirmed the presence of endangered eulachon (Thaleichthys pacificus) across three fjords and identified deep fjord habitats as conservation priorities for mesopelagic species, including sensitive elasmobranchs and diel vertical migrators such as northern lampfish (Stenobrachius leucopsarus). eDNA peaks for several CPS during winter and spring matched documented spawning windows, underscoring the importance of fjords as seasonal spawning habitat. This globally transferable approach can supplement local stewardship initiatives and long-term monitoring efforts, contributing to more effective marine conservation area design and management.