Changes in the structure and dynamics of sandy beach macrofaunal populations result from the simultaneous action of local and regional factors acting synergistically. This is particularly noticeable in transitional interfaces between freshwater and marine ecosystems, where large-scale gradients affect local beach morphodynamics and resident fauna. The wedge clam Donax hanleyanus occurs on beaches with contrasting morphodynamics along the salinity gradient generated by the Rio de la Plata estuary. We conducted sampling surveys to etermine a fine-grained comprehensive coverage of the species’ distribution in Uruguay to assess the concurrent effects of large-scale variations in salinity and local beach morphodynamics on wedge clam populations along 400 km (16 sandy beaches) over 2 yr. The main factor controlling wedge clam occurrence was salinity, overriding the effects of local habitat features. On beaches where the species was present, total abundance was higher on oceanic dissipative shores, which also harbored a higher abundance and relative representation of recruits. Recruitment was almost lacking in reflective beaches. However, biomass of adults with larger body sizes prevailed on reflective beaches, suggesting a scaling of abundance to body size and potential density-dependent effects. In this metapopulation, estuarine beaches are sinks, whereas oceanic beaches act as source habitats. We concluded that large-scale gradients generated by salinity variations translated into local population patterns (distribution, abundance and population structure) and processes (recruitment), which were secondarily driven by local morphodynamics. The relative importance of pre- and post-settlement processes across the morphodynamic spectrum from reflective to dissipative beaches has yet to be elucidated.