In the life of the endangered but still fished Anguilla anguilla, glass eels are recruited through estuaries. These fragile ecosystems are among the most disturbed on the planet. Here, heavy metals and microplastics were measured in estuary water and European glass eels entering bay of Biscay rivers of different size and anthropogenic stress. Eels from all the estuaries exhibited cadmium exceeding legal European limits, as happened with lead in samples from the highly disturbed Avilés estuary. Several water samples from small rivers surpassed the estimated limit of microplastic for ecotoxicological safety. In multiple regression analysis, both eel lead and microplastic content were significantly explained from shipping activity in the estuaries. Eel cadmium content was not associated with estuary stressors, being probably acquired during the oceanic migration of eel larvae. The presence in eels of new white polyethylene particles that had not been found previously in the region could be explained from the marine plastic spill of "Toconao" cargo in December. The same spill could explain a significant increase of microplastic bioconcentration in the glass eels in comparison with previous surveys. These risks for critically endangered eels, and for the consumers, highlight the urgent need for reducing the impact of contaminants on both local and global scales.