In this paper we present sedimentological, geochemical, mineralogical and 14C Accelerator Mass Spectrometry (AMS) dating data of a 21.0-m core obtained from Alikes Lagoon, Zakynthos Island. It is the first time that sedimentological and geochemical data are presented, up to 21-m depth, from an Holocene coastal lagoon environment of the Ionia Sea, western Greece. The sedimentological properties and the geochemical composition of sediments were studied for the time period between 8540 years bp to present. Samples were analysed for their particle size, calcium carbonate and total organic carbon (TOC) content. Moreover, bulk sample chemical analyses for major and trace elements were carried out, as well as bulk, oriented mineralogical analyses for the clay fraction (<2 µm) were determined by powder X-Ray diffraction. The grain size characteristics, statistical parameters and TOC, for the Holocene analysed samples, suggest a coastal environment (restricted-shallow) with reduced salinity such as a tidal flat and/or particularly marsh in a lagoon margin. Sediment characteristics as well as trace element records may contain additional new palaeoclimate information that provide important new constraint on sediment depositional environment and Holocene climate. Stratigraphic variation of geochemical indices, such as Rb/Ti, Cs/Ti, Eu/Eu*, Th/Ti, La/Ti, Ta/Ti, Yb/Ti and Y/Ti, for the sediments with ages from 8540 to 7210 years bp, remain relatively constant indicating that the provenance of the Alikes Lagoon remained similar throughout the mid Holocene. However, geochemical indices in sediments with ages from 7110 years bp to present, indicate the transition from a warm and wet climate in the middle Holocene to a relatively cold climatic conditions in modern times. Copyright © 2012 John Wiley & Sons, Ltd.