Trace element accumulation is particularly important in coastal and transitional environments, which act as contaminant buffers between the continental and marine systems. We compared trace element transfer to the biota in two locations with different open-sea exposures in a semi-enclosed marine coastal area (Stagnone di Marsala, Sicily, Italy) using isotopically reconstructed food chains. Samples of sediment, macroalgae, seagrasses, invertebrates, fish, and bird feathers were sampled in July 2006 and analysed for stable carbon and nitrogen isotopes (δ(13)C, δ(15)N) and trace elements (arsenic [As], cadmium [Cd], total mercury [THg], and lead [Pb]). Trophic magnification factors were calculated through the relationships between trace elements and δ(15)N in consumers. As and Pb were greater in organic matter sources (sediments and primary producers), whereas Cd and THg were greater in bird feathers. At the food chain level, an insignificant trophic transfer was found for all elements, suggesting biodilution rather than biomagnification. Sediments were more contaminated in the location with lower open-sea exposure. Macroalgae and seagrasses overall mirrored the spatial pattern highlighted in sediments, whereas differences between the two locations became further decreased moving toward higher trophic levels, indicating that trophic transfer of sediment and macrophyte-bound trace elements to the coastal lagoon food chain may be of relatively minor importance.