This dataset contains biological and environmental data collected in the S’Ena Arrubia Lagoon (Sardinia, Italy) during two winter (February–March 2021) and two summer (June–July 2021) sampling campaigns. Six stations were selected across areas with different degrees of confinement, proximity to freshwater inflows, and marine influence. At each station, replicate sediment samples were collected using a box corer to analyze macrozoobenthic assemblages and the quantity, biochemical composition, and nutritional quality of sedimentary organic matter (OM). Water temperature, salinity, and dissolved oxygen were also measured. Macrozoobenthos were identified to the lowest possible taxonomic level, counted, and preserved. The dataset provides insights into spatiotemporal patterns of benthic communities and their relationship with sedimentary OM in a Mediterranean eutrophic coastal lagoon, supporting ecological assessments and management of transitional ecosystems