During the second half of the twentieth century, coastal lagoons in densely populated regions experienced eutrophication due to excessive nutrient inputs. Detrimental effects, including hypoxia/anoxia and harmful algae blooms, have occurred in many Mediterranean lagoons, but their trophic evolution is poorly documented. The lack of adequate monitoring data can partly be offset by examining sedimentary records. In the Mar Piccolo, a lagoon comprising two basins near Taranto (Italy), eutrophication has followed population growth and pollution resulting from naval activities and massive industrialisation. Based on 210Pb-dated sediment cores, continuous in situ density profiles obtained with computed tomography, organic carbon (OC) and total nitrogen (TN) content and OC and TN isotopic signatures, this paper reconstructs the history of eutrophication, discusses the sources of organic matter and provides an estimate of the OC burial rate before and during the eutrophic period. OC burial increased in the period 1928–1935 and peaked in the decade 1960–1970. OC and TN content were still high in the surface sediments collected in 2013, despite partial diversion of sewage outfalls in the period 2000–2005. The divergent δ13C and δ15N signatures of the two basins during the eutrophic period suggest they were affected by different nutrient sources. The OC burial rate during the eutrophic phase (≈ 46 g m−2 y−1) was close to the world median value for lagoon sediments, and was about twice the burial rate recorded in the preceding oligotrophic phase.