Ecuador’s Galapagos Islands and their unique biodiversity are a global conservation priority. We investigated the presence, partitioning and environmental drivers of plastic contamination across the marine ecosystem, designing a systematic risk scoring analysis to identify the most vulnerable species. Beach contamination varied by site (macroplastic 0 - 0.66 items.m-2, large microplastics 0 - 448.8 particles.m-2, small microplastics 0 – 74.6 particles.kg-1), with high plastic accumulation on east-facing beaches indicating input from the Humboldt Current. Local littering and waste management leakages accounted for 2% of macroplastic. Microplastics (including synthetic cellulosics) were prevalent in sediments (6.7 - 86.7 particles.kg-1) and surface seawater (0.04 - 0.89 particles.m-3), with elevated concentrations in the harbour suggesting local input. Microplastics were present in all seven marine invertebrate species examined, found in 52% of individuals (n = 123). Risk scoring identified 32 species in need of urgent, targeted monitoring and mitigation including pinnipeds, seabirds, turtles, sharks and corals.