Many studies have evaluated bird mortality in relation to roads and other human structures, but little is known about the potential impacts of railways. In particular, it is uncertain whether railways are an important mortality source when crossing wetlands heavily used by aquatic birds. Here we analyze bird collisions in a railway that crosses the Nature Reserve of the Sado Estuary (Portugal) over an annual cycle, documenting bird mortality and the flight behaviour of aquatic birds in relation to a bowstring bridge. During monthly surveys conducted on 16.3 km of railway, we found 5.8 dead birds/km/10 survey days in the section crossing wetland habitats (6.3 km), while <0.5 dead birds/km/10 survey days were found in two sections crossing only forested habitats. Most birds recorded were small songbirds (Passeriformes), while there was only a small number of aquatic birds (common moorhen, mallard, flamingo, great cormorant, gulls) and other non-passerines associated with wetlands (white stork). During nearly 400 h of observations, we recorded 27,000 movements of aquatic birds across the Sado bridge, particularly in autumn and winter. However, only <1% of movements were within the area of collision risk with trains, while about 91% were above the collision risk area, and 8% were below the bridge. Overall, our case study suggests that bird collisions may be far more numerous in railways crossing wetland habitats than elsewhere, although the risk to aquatic birds may be relatively low. Information from additional study systems would be required to evaluate whether our conclusions apply to other wetlands and railway lines.