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Bioaccumulation and biomagnification of anthropogenic particles are crucial factors in assessing microplastic impacts to marine ecosystems. Microplastic pollution poses a significant threat to iconic and often endangered species but examining their tissues and gut contents for contaminant analysis via lethal sampling is challenging due to ethical concerns and animal care restrictions. Incorporating empirical data from prey items and fecal matter into models can help trace microplastic movement through food webs. In this study, the Galápagos penguin food web served as an indicator species to assess microplastic bioaccumulation and biomagnification potential using trophodynamic Ecopath with Ecosim (EwE) modelling with Ecotracer. Empirical data collected from surface seawater near Galápagos penguin colonies, zooplankton, penguin prey, and penguin scat in October 2021 were used to inform the ecosystem model. Multiple scenarios, including a 99% elimination rate, were employed to assess model sensitivity. Model predictions revealed that microplastics can bioaccumulate in all predator-prey relationships, but biomagnification is highly dependent on the elimination rate. It establishes the need for more research into elimination rates of different plastics, which is a critical missing gap in current microplastic ecotoxicological and bioaccumulation science. Compared to empirical data, modelling efforts underpredicted microplastic concentrations in zooplankton and over-predicted concentrations in fish. Ultimately, the ecosystem modelling provides novel insights into potential microplastics' bioaccumulation and biomagnification risks. These findings can support regional marine plastic pollution management efforts to conserve native and endemic species of the Galápagos Islands and the Galápagos Marine Reserve. [ABSTRACT FROM AUTHOR]