The purpose of this thesis is to study the « source-to-sink » system of the Pyrenees system and its retro-foreland basins, the Aquitaine basin and its deep equivalent, the Bay of Biscay during the Cenozoic. This work required (1) a biostratigraphic re-evaluation, (2) an analysis in terms of seismic stratigraphy and quantification of preserved sediment volumes, (3) a quantification of eroded volumes from the Massif Central, (4) a quantification of the eroded volumes from the Pyrenees, (5) a synthesis of all these data. The transition from the orogenic to the post-orogenic phase occurs between 27.1 and 25.2 Ma. It corresponds to the succession of three erosional surfaces that fossilize the entire compressive structures. The orogenic period is divided into two phases, (1) up to 43.5 Ma (Lutetian), is characterized by a strong subsidence at the front of the North-Pyrenean-Thrust, (2) from 43.5 to 27.1 Ma, is characterized by the subsidence migration toward the basin, in sub-basins controlled by the thrusts activity. The post-orogenic period is divided into two phases, (1) from 25.2 to 16 Ma approximately, corresponds to the establishment of the isostatic rebound, (2) between 16 and 10.6 Ma, corresponds to an uplift of the whole system. This phase corresponds to a West European event undoubtedly linked to a mantle activity.