Passive margins are characterised by an important tectonic and thermal subsidence, which favours a good preservation of sedimentary sequences. This sedimentation in turn enhances the subsidence because of loading effects. We present here a direct method based on sedimentary markers seen on seismic data, to evaluate total subsidence rates from the coast to the outer shelf and to the deep basin in the Gulf of Lion, from the beginning of massive salt deposition up to present day (the last circa 6 Ma) with minimal theoretical assumptions. On the shelf, the Pliocene-Quaternary subsidence shows a seaward tilt reaching a rate of 240 m/Ma (±15 m/Ma) at the shelf break (70 km from the present day coastline) (i.e. a total angle of rotation of 0.88° (0.16°/Ma)). We were also able to measure and quantify for the first time the isostatic rebound of the outer shelf due to the Messinian salinity crisis (MSC). This value is very high and reaches up to 1.3 km of uplift during the crisis around the Herault–Sète canyon heads (around 1.8 km/Ma). On the slope, we also find a seaward tilting subsidence from Km 90 to Km 180 with a measured angle of 1.41°. From 180 km to the deepest part of the basin, the total subsidence is then almost vertical and reaches 960 m/Ma (±40 m/Ma) during the last 5.7 Ma (±0.25 Ma) in the deepest part of the basin. The subsidence is organised in three compartments that seem related to the very deep structure of the margin during the opening of the Liguro-provencal basin. These very high total subsidence rates enable high sedimentation rates along the margin with sediments provided by the Rhône river flowing from the Alps, which in turn enable the detailed record of climate evolution during Pliocene-Quaternary that make of the Gulf of Lion a unique archive.