This dataset, generated through trophodynamic Ecopath with Ecosim (EwE) modeling and Ecotracer, encompasses two models—a novel model by McMullen K. (2023), featuring the Galápagos penguin as a sentinel species for microplastics in the Galápagos Marine Reserve, and a model by Ruiz DJ and Wolff M (2011) focusing on the Bolivar Channel ecosystem. Empirical data was collected in October 2021 (McMullen K., 2023), including surface seawater, zooplankton, penguin prey, and penguin scat. This empirical data and other data from available literature feed the model. Various scenarios, notably a 99% elimination rate, were employed to gauge model sensitivity. Results indicate that microplastics can accumulate in predator-prey relationships, with biomagnification contingent on elimination rates. This underscores the urgent need for further investigation into the elimination rates of distinct plastics, addressing a crucial gap in contemporary microplastic ecotoxicology and bioaccumulation research. The dataset offers valuable insights into the complex dynamics of plastic pollution in marine ecosystems, urging heightened scrutiny of plastic elimination rates for informed conservation strategies. For methods see McMullen K. (2023). References:  McMullen K. The Galápagos penguin as the “canary in the coal mine” for microplastics research in the Galápagos Marine Reserve & plastic pollution perceptions in Ecuadorian mangrove communities. M.Sc. Thesis. University of British Columbia. 2023. Available from: http://hdl.handle.net/2429/84664 Ruiz DJ, Wolff M. The Bolivar Channel Ecosystem of the Galapagos Marine Reserve: Energy flow structure and role of keystone groups. J. Sea. Res. 2011 Aug;66(2):123–34.