Plastic pollution is a major ecological catastrophe that endangers vulnerable species. Small plastic fragments and filaments enter the food web in the ocean threatening marine species health. Here microplastics between 0.5 and 5 mm were quantified from eight beaches of southwest Bay of Biscay (Spain) within Natura-2000 Special Protection Areas for birds. Sand samples were taken using a randomized quadrat-based protocol. Between 145 and 382 particles per kg of dry sand were found, which is relatively high in comparison with other European beaches. Microfibers were more abundant than microplastics. PERMANOVA revealed a significant effect of the beach location (inside versus outside the estuary). Open beaches contained a higher microplastic density than sheltered ones suggesting that many beached microplastics come from the ocean. Birds are at risk in the studied protected spaces as revealed from high concentrations of fibres in depositions of European shag and gulls.