This paper presents an integrated approach to assess Holocene environmental changes in the Sperchios delta, Sperchios rift, central Greece. A multidisciplinary study was carried out applying established analytical methods as well as exploring new techniques to detect past environmental conditions in a fluvio-deltaic depositional system. A series of six deep boreholes, up to 50 m long, and four shallow cores, up to 6 m long, from across the delta plain, were studied in detail. Sedimentary facies were defined by changes in grain size and macro- and microfaunal composition. Variability in mineral magnetic composition documented by changes in bulk magnetic susceptibility (χ and χ_77K/χ_293K) and remanence parameters ( S₋₃₀₀ and σARM/σSIRM ratios), as well as down-core elemental variations obtained by scanning micro-x-ray fluorescence (µ-XRF), provide constraints on the depositional changes related to the evolution of the Sperchios delta. Correlations between elemental data derived by µ-XRF analyses and grain size were also analyzed and used to further constrain the facies interpretation. Overall, these Holocene sediments reveal a transgressive–regressive succession overlying pre-transgressive terrestrial deposits of Late Pleistocene–Early Holocene age. Furthermore, 13 new ¹⁴C radiocarbon dates constrain the transgression rate to be ~3.5 m/yr for the Early Holocene and the regression rate to be ~1 m/yr for the Late Holocene. The Sperchios delta plain developed when the rate of sea-level rise decreased ~6000 cal. yr BP as it has been proposed for the broader area of Aegean Sea. This study demonstrates that the combination of techniques used here provides a powerful way to map out paleoenvironmental changes and thus the 3D stratigraphic architecture of Holocene sedimentary successions.