We investigated macrofaunal species richness and composition in Posidonia oceanica, Cymodocea nodosa and Leaf litter beds within a coastal area of the Gulf of Oristano in proximity of the Cabras lagoon (western Sardinia, Italy). A total of 124 taxa were found, of which 116 were identified at the species level. They were analyzed based on both taxonomic and substrate affinity classification. Presence/absence analysis revealed that P. oceanica, C. nodosa and Leaf litter were all characterized by a conspicuous number of soft-bottom polychaetes (e.g., Prionospio multibranchiata and Ampharete acutifrons) and crustaceans (e.g., Corophium sextonae and Dynamene bidentatus), also known as detritivores. There were also major differences between the three habitats investigated. Consistent with its structural complexity, P. oceanica showed the highest species richness [E(S50)] and the most diversified macrofaunal assemblages, both in terms of taxonomic groups and taxa associated with different substrates. The two seagrasses, however, showed a similar species composition and differed from Leaf litter for the exclusive presence of hard-bottom species (e.g., the tunicate Phallusia fumigata) and seagrass-associated species (e.g., the polychaete Syllis garciai and the decapod Paguristes syrtensis). In contrast, Leaf litter showed the most differences between the habitats, and was characterized by the bivalves Abra alba and Cerastoderma glaucum, not found in seagrass beds, and by Loripes lacteus and Ruditapes decussatus. Leaf litter also had the highest content of organic matter (26.7% ± 1.4) and total organic carbon (10.3% ± 0.4). Our results confirmed the facilitative role of living seagrasses, in particular P. oceanica, as related to their structural complexity, for numerous species from different substrates (e.g., hard bottom species). This study also showed that leaf litter beds act as a particular environment where sediment instability, leaf breakdown, and organic matter enrichment and decomposition strongly influence animal distribution. Finally, our results highlighted the ecological and trophic importance of seagrass-derived detritus and the associated macroinvertebrate detritivores within seagrass-dominated systems.