Migratory shorebirds are exposed to a wide range of pathogens along their migratory flyways, but their capacity to acquire or spread pathogens beyond endemic areas is poorly known. We focused on the spillover and acquisition of mosquito-borne pathogens such as haemosporidians and West Nile virus (WNV) on key-staging Iberian wetlands during different seasons. We screened seven shorebird species (447 individuals), and detected low haemosporidian prevalence (0.6%). Furthermore, no WNV infections could be detected, though 6.2% revealed antibodies against flaviviruses. Although Iberian wetlands congregate numerous shorebirds of different species and origins, the potential introduction of foreign pathogens is not a common event.