This study presents sedimentological, palaeoecological and geochemical data from a shallow Mediterranean coastal lagoon which has been severely influenced by human intervention over the last 70 years. The Gialova Lagoon is protected by international conventions and is listed in the Natura 2000 European Community Network as Special Protection Area (SPA) and Site of Community Importance (SCI). The spatial variability of sediment characteristics such as grain size, total organic carbon (TOC) and moment measures, mean, sorting, kurtosis and skewness were calculated. Moreover, micro- and macrofossil and sediment geochemical analyses were carried out on six gravity core samples. Study of the above parameters indicates that the anthropogenic impact and intervention are reflected in the micro- (ostracods, foraminifera, charophytes) and macrofossil (molluscs) taxa corresponding to different depositional environmental facies, representing a brackish lagoon with the influence of (a) fresh water inflow, (b) shallow marine environment and (c) hypoxic and dystrophic conditions. The geochemical characteristics and the calculation of the degree of sediment contamination using enrichment factors (EF), contamination factors (Cif) and the index of geo-accumulation (Igeo) indicate a recent relative improvement of the lagoon towards the upper layers of the gravity cores, rendering the lagoon as unpolluted to moderately polluted. This combinatorial study of sediment geochemical characteristics, as well as the downcore micro- and macrofossil assemblages, can be considered as a baseline for future monitoring in accordance with European Union directives, and for any future engineering interventions for the lagoon environmental maintenance and conservation; as this is the first time that geochemical and downcore palaeoecological data have been presented from this lagoon.