This thesis presents a multi-proxy reconstruction from 5 different coastal wetlands of southern Greece spanning in the Holocene period and an in-depth review and application of non-destructive systems (CT scanning, X-ray Fluorescence) in paleoenvironmental research. During this thesis, the acquired dataset used consisted of a) X-ray Fluorescence scanning (XRF), b) Computed Tomography (CT) scanning, c) Stable isotopes δ18O and δ13C, d) micropaleontology (foraminifera, ostracods, diatoms, pollen), e) mineralogical analysis, and f) standard sedimentological techniques (grain size, magnetic susceptibility (MS), Total Organic Carbon (TOC), carbonates content). The chronological framework for the sediment cores was established through 14C radiocarbon dating. The wetlands studied are Aliki salt pond (NE Gulf of Corinth), Klisova lagoon (SW Greece), lake Vouliagmeni (E Gulf of Corinth), Agoulinitsa marsh field (W Peloponnese) and Pappas lagoon (NW Peloponnese). The sites form an E-W transect of southern Greece, an area with high climatic and environmental spatial variability, whereas human occupancy on all areas is recorded from antiquity. Non-destructive, high-resolution techniques used in this thesis have been established as standard in the last decades and have been a great asset in geosciences. Computed Tomography (CT) was conducted in lake Vouliagmeni, Agoulinitsa marsh and Pappas lagoon cores. In contrast, XRF was performed on all core sections except for Pappas lagoon core, where the high assemblage of bivalve shells could lead to bias of Ca. The fundamental parameter behind CT analysis is the Hounsfield units that reflect relative density variations in the sediment. Correlation between HU values and heavy elements like Zr has been detected in all cores, whereas distinct sedimentological facies were recorded according to HU variations. In Agoulinitsa and Pappas lagoon, microstructural characteristics like shells/sediment ratio and root remnants were examined through 3D sections, in which HU boundaries were set accordingly. Lake Vouliagmeni sediment core was characterized by extreme stratigraphic variations with lamination structures alternating with homogenous deposits and event layers. Laminae thickness and boundaries were recorded through 3D rendered volumes with HU boundaries. Micro CT scanning and thin section analysis was also performed to cross-check possible variations. Event sedimentation layers were distinguished through the combined use of CT scanning, XRF and MS, with layers responding to increased HU, MS and Mn values. Statistical assessment of elemental distribution and HU revealed 3 different clusters. Cluster A responded to sedimentation during enhanced evaporation in the area, Cluster B emulated sedimentation during increased chemical weathering in the catchment, and Cluster C reflected the homogenous deposits. Aliki salt pond is located in a highly tectonic region, at the northeast part of the Gulf of Corinth in Greece. Beachrock deposits that form a barrier between the salt pond and the marine environment play an essential role in the evolution of the area. The chronological framework was set at ca. 3100 cal BP by four 14C radiocarbon dates and the established evolutionary model indicate four different changes taking place during this period in the study area. From around 3100 to 1600 cal BP, a transition from a closed to an open lagoonal environment, was identified, interrupted by a terrestrial fluvial deposit at ca. 2500 cal BP. A shift toward a closed lagoonal system at around 1600 cal BP and the establishment of a salt pond environment seem to correlate with tectonic activity. The study provides important information about the evolution of the coastal landscape in such an active tectonic region and points the interaction between regional human activity and climatic changes during the late-Holocene period.Klisova lagoon is located in the eastern part of Messolonghi-Etoliko wetland, the biggest lagoonal complex of Greece and an area of great environmental interest. For the last 4700 cal BP, the freshwater influx, the progradation of the Evinos river delta and related geomorphological changes control the environmental conditions (e.g. depth and salinity) in the lagoon system. Considering the centennial temporal resolution of our analyses, small offsets of c.a. 50 years due to the lack of regional reservoir correction do not impact the reported radiocarbon ages considerably. Prior to 4000 cal BP, a relatively shallow water depth, significant terrestrial/freshwater input and increased weathering in the lagoon area are inferred. Elemental proxies and increased dinoflagellate and foraminifera abundances, which indicate marine conditions with prominent freshwater influxes, point to the gradual deepening of the lagoon recorded at the drilling site up to 2000 cal BP. The marine and freshwater conditions equilibrium sets at 1300 cal BP, and the lagoonal system seems to reach its present state. Maxima of anthropogenic pollen indicators during the Mycenaean (3200 cal BP), Hellenistic (2200 cal BP) and Late Byzantine (800 cal BP) periods suggest intervals of increased anthropogenic activities in the study area. Lake Vouliagmeni is subjected to intense climatically and tectonic forces, causing stratigraphic variations, with laminated sediments frequently interrupted by homogenous and event sedimentation deposits. Lamination couplets consist of aragonite layers alternating with detrital and organic residues and form during periods of seawater intrusion and stratification of the lake water. The discontinuous occurrence of laminated deposits excludes a varve based chronology from being established but still highlights the susceptibility of the lake to record environmental and climatically driven changes. Our synthesis model for regional climatic reconstruction and local environmental changes derives from δ18O and δ13C data from the laminated and homogenous sediments studied separately depending on the dominant carbonate mineral. This is further strengthened by high-resolution geochemical proxies, diatom and sedimentological data. Regional climatic trajectories from key sites and possible links to the lake Vouliagmeni record are explored in response to atmospheric circulation patterns variations. Phases of overall humid conditions are recorded by the increased inflow of siliciclastic material in the lake and negative δ18Obulk values. In contrast, periods of marine intrusion and enhanced evaporation are recorded by aragonite precipitation, increased δ18OAr values and laminations. The driving mechanism behind laminae formation seems to be marine intrusions, leading to pycnocline stabilization and increased evaporation of lake surface waters during summer months. Climatic oscillations recorded during the Holocene, apart from their duration, do not exceed events of the last millennia.