A comprehensive sedimentological study was undertaken in the Miocene of the subalpine massifs and southern Jura (France) with the aim to constrain the evolution of process changes in third-order sequences of peripheral foreland basins during the overfilled phase (i.e. sediment supply higher than accommodation space). Fieldwork analyses based on 35 sedimentological sections allowed the identification of four depositional models: wave dominated, mixed wave-tide, river to tide and river dominated. The sections were dated using chemostratigraphy (i.e. marine strontium isotopic ratios), revealing three-third-order sequences between the Upper Aquitanian and the Langhian. Chronostratigraphical and sedimentological results document prominent and recurrent changes in depositional models along third-order sequences: (i) in the earliest stage of the transgression, mixed-energy coastal environments influenced by the local coastal morphology prevailed (in palaeo-highs or incised valleys); (ii) during the course of the transgression, Gilbert delta deposits suggest a prominent steepening linked to a tectonic uplift in the proximal depozone (between the tectonically active frontal part of the orogenic wedge and the proximal foredeep). Instead, in the distal depozone (between the proximal foredeep and the proximal border of the flexural uplifted forebulge), deposits were characterized either by wave-dominated or mixed wave-tide environments and are likely eustatically-driven; (iii) during the maximum flooding stage, water depth remained shallow below the storm-weather wave base; and (iv) during the regression, the proximal depozone is characterized by the progradation of gravel-rich fan deltas. In the distal depozone, mixed wave-tide systems preceded the development of river to tidal depositional environments. These results were integrated and compared with facies models from other basin analogues worldwide. A model tackling the evolution of process changes within third-order sequences (of the overfilled phase) of foreland basins is proposed, thereby improving sequence stratigraphic predictions in foreland basins.