Late Quaternary sedimentary cover in the Thermaikos Gulf consists of three seismic Units: (i) the uppermost Unit A that represents delta progradation during the last 6000 yr when the sea surface almost reached the present level (Highstand Systems Tract, HST); (ii) Unit B that includes relatively coarse-grained sediments deposited in a shallow, high-energy, estuarine environment during the post-glacial transgression (Transgressive Systems Tract, TST); and (iii) the lowest Unit C which may represent late glacial prodeltaic deposits and slope to basin turbidites (Lowstand Systems Tract, LST). Seismic units A and B overlay a well-defined unconformity which resulted from sub-aerial erosion during the late glacial sea-level fall. Subtracting the thickness of Unit A from the present bathymetry, the paleo-relief of the Late Holocene times (ca. 6000 yr BP, sea level up to − 20 m) was assessed. Similarly, the paleo-relief ∼24 000 yr BP (sea level − 100 to − 120 m) was estimated. The main morphological feature is the incised valley of a major river that resulted from the confluence of the Axios, Aliakmon, Loudias, Gallikos and possibly Pinios Rivers. Sediment fluxes in the NW Aegean Sea were estimated for three time spans of the Late Quaternary (Interval I: 6000 yr BP–present, Interval II: 18 000– 6000 yr BP and Interval III: ∼24 000–18 000 yr BP). The terrestrial sediment load supplied by the Axios, Aliakmon, Pinios, and smaller rivers, was estimated at 35.4 × 10 9 t for Interval I. 93% of this material was deposited on the continental shelf, whereas the remaining 7% was transported to the adjacent basin. The mean annual terrestrial flux was estimated at 5.5 × 10 6 t yr − 1 . During Interval II, more than 79 × 10 9 t of terrestrial sediment were discharged into the area (terrestrial flux 6.6 × 10 6 t yr − 1 ), of which 86% was deposited on the shelf. During Interval III, the terrestrial load was 40.6 × 10 9 t (terrestrial flux 6.8 × 10 6 t yr − 1 ), and sediments were predominantly deposited on the slope and basin. Based on the sediment's carbonate content, the biogenic loads and fluxes were also determined. The biogenic flux during Intervals II and III was found to be ∼2.5-times higher than during Interval I.