Incidental catch of non-target species (bycatch) is a major barrier to ecological and economic sustainability in marine capture fisheries. Key to mitigating bycatch is an understanding of the habitat requirements of target and non-target species, and the influence of heterogeneity and variability in the dynamic marine environment. While patterns of overlap among marine capture fisheries and habitats of a taxonomically diverse range of marine vertebrates have been reported, a mechanistic understanding of the real-time physical drivers of bycatch events is lacking. Moving from describing patterns towards understanding processes, we apply a Lagrangian analysis to high-resolution ocean model output to elucidate the fundamental mechanisms that drive fisheries interactions. We find that the likelihood of marine megafauna bycatch is intensified in attracting Lagrangian Coherent Structures (LCS) associated with (sub-)mesoscale filaments, fronts and eddies. These results highlight how the real-time tracking of dynamic structures in the oceans can support fisheries sustainability and advance ecosystem-based management.Managing the competing demands of resource extraction and biodiversity conservation is a central challenge in maintaining ecosystem function across terrestrial and marine systems 1, 2 . In the oceans, over-harvesting, habitat degradation, and bycatchincidental catch that is unwanted, unused or unmanaged 3 -are global-scale barriers to fisheries sustainability. Seafood is a major protein source for more than three billion humans worldwide 4 , and the importance of a sustainable supply will increase with the rapidly rising global population 5 . Prioritising the ecological sustainability of marine fisheries is crucial to prevent ecosystem collapse and protect food sources and future livelihoods in fisheries-reliant communities 6, 7 . Non-target catch represents an estimated 40% by mass of all marine catch 3 , and has been identified as the most serious global threat to a diverse array of marine vertebrates including sea turtles, seabirds, marine mammals, pinnipeds and elasmobranchs 3,8,9,10 . Marine megafauna populations face a range of cumulative anthropogenic stressors, particularly in coastal zones under intensive human use 10 , and many are of immediate conservation concern 12, 13, 14 . Life history characteristics such as long life-span, low fecundity, late maturity and wide-ranging movements exacerbate the ecological impacts of fisheries bycatch, as populations struggle to buffer anthropogenic pressure. The removal of high-trophic level species, described as trophic downgrading 15,16 , causes substantial changes in ecosystem function 14 , and reduces the profitability of fisheries 5 . To halt or reverse these trends, bycatch mitigation measures such as changes to fishing gear and practice, fishing effort reallocation and re-distribution have been successfully implemented in many fisheries 17,18 . However, the relative success of these mitigation options relies upon management effort being both well-target...