The Karpatian deposits of the central part of the Carpathian Foredeep in Moravia, which are deeply buried under the Outer Western Carpathians, provide a unique opportunity to reconstruct the former evolutionary stages of this peripheral foreland basin and its paleogeography. A succession of three depositional units characterized by a distinct depositional environment, provenance, and partly also foreland basin depozone, have been identified. The first depositional unit represents a proximal forebulge depozone and consists of lagoon-estuary and barred coastline deposits. The source from the “local” crystalline basement played here an important role. The second depositional unit consists of coastline to shallow marine deposits and is interpreted as a forebulge depozone. Tidalites recognized within this unit represent the only described tide-generated deposits of the Neogene infill of the Carpathian Foredeep basin in Moravia. The source from the basin passive margin (the Bohemian Massif) has been proved. The third depositional unit is formed by offshore deposits and represents a foredeep depozone. The provenance from both passive and active basin margin (Silesian Unit of the Western Carpathian Flysch Zone) has been proved. Thus, both a stepwise migration of the foredeep basin axis and shift of basin depozones outwards/cratonwards were documented, together with forebulge retreat. The shift of the foreland basin depozones more than 50 km cratonward can be assumed. The renewed thrusting along the basin’s active margin finally completely changed the basin shape and paleogeography. The upper part of the infill was deformed outside the prograding thrust front of flysch nappes and the flysch rocks together with a strip of Miocene sediments were superposed onto the inner part of the basin. The width and bathymetric gradient of the entire basin was changed/reduced and the deposition continued toward the platform. The basin evolution and changes in its geometry are interpreted as a consequence of the phases of the thrust-sheet stacking and sediment loading in combination with sea-level change.