Pialassa Baiona is a shallow temperate coastal lagoon influenced by a variety of factors, including regional climate change and local anthropogenic disturbances. To better understand how these factors influenced modern organic carbon (OC) sources and accumulation, we measured OC as well as stable carbon isotopes (d¹³C) in ²¹⁰Pb-dated sediments within a vegetated saltmarsh habitat and a human impacted habitat. Relative Sea Level (RSL) at the nearby tide gauge station data and four different Sea Surface Temperature (SST) data sets were analyzed starting from 1900 to assess the potential effect of sea ingression and warming on the coastal lagoon sedimentary process. The source contribution calculated from the MixSIAR Bayesian model revealed a mixed sedimentary organic matter (OM) composition dominated by increasing marine-derived OM after the 1950s, parallel with decreasing autochthonous saltmarsh vegetation (Juncus spp.) in the saltmarsh habitat and riverine-estuarine-derived OM in the impacted habitat. RSL rise in the area (8.7±0.5 mm yr⁻¹ in the period 1900-2014) has been mainly driven by the land subsidence, especially during the central decades of the last century, enhancing the sea ingression in the lagoon. Annual SST anomalies present, starting from the eighties, a continuous warming tendency from 0.034±0.01 to 0.044±0.009°C yr^-1. No direct effect on sedimentary properties was detected; however, RSL influenced OM sediment properties, although this effect was different between the two habitats.