The trophic fate of various food sources is of central interest for ecologists, yet not well understood in coastal lagoon food webs. In this field study, fatty acids (FA), stable isotopes (SI), and compound-specific isotopic analysis (CSIA) on FA were used to investigate how diets from oceanic and local sources are retained in a bivalve species (Spondylus crassisquama; Lamarck 1819) along a transect in the Ojo de Liebre lagoon (BCS, Mexico). Results from SI and FA indicated the contribution of oceanic diatoms at the entrance of the lagoon, through 15N enrichment, and higher proportions of 16:1n-7 and 20:5n-3 in digestive glands. In the inner bay, higher abundance of 18-carbon FA (18:1n-9, 18:3n-3, 18:4n-3) suggested a higher contribution of microheterotrophs, including (dino)flagellates and ciliates, to the diet of this bivalve derived from local production. Significant spatial differences for the δ13C of FA highlighted changes in the origin of food sources. Indeed, a 13C depletion was observed in the δ13C of heterotrophic flagellates biomarkers in individuals from the innermost station, revealing that their origin in the diet of bivalves differs within the lagoon, highlighting the importance of local processes (sediment resuspension, remineralization) in the trophic functioning of the lagoon. The δ13C values of FA considered as diatoms biomarkers (16:1n-7 and 20:5n-3) were consistent, which suggests that diatoms assimilated have very similar origins throughout the lagoon. The complementary of the tracers used here allowed for a better understanding of the trophic functioning of this coastal lagoon submitted to oceanic influences.