Understanding the nature and origins of food sources supporting coastal lagoon-inhabiting organisms is necessary to evaluate the ecological status of such ecosystems. The trophic ecology of a bivalve specie Spondylus crassisquama was studied in the Ojo de Liebre lagoon (Baja California, Mexico), combining stable isotope (SI), fatty acid (FA) and sterols analyses along a transect under oceanic influences. The second objective of the study was to investigate if sterols compositions give complementary information to those obtained from FA and SI. Temporal and spatial patterns of the three biomarkers in bivalve tissues suggest oceanic inputs at the mouth of the lagoon, while the inner station was characterized by a contribution of local sources including an important role of micro heterotrophs. This study revealed that the association of lipid biomarkers provide higher taxonomic resolution of the spatiotemporal heterogeneity in nutrient sources influencing the trophic functioning of a large coastal lagoons.