Despite increasing knowledge on the orogenic phases of the Pyrenees, the Neogene evolution of the range remains poorly constrained. The central Pyrenees, particularly the Ariège River valley and its terrace systems and glacial extensions, are key to reconstructing Pyrenean evolution during the Neogene. However, few terrace relics remain on the piedmont edges. To overcome this limitation and temporally extend the dataset obtained from terraces, we focus on alluvium-filled horizontal epiphreatic passages developed in limestone karstic networks. These landforms record the transient position of former local base levels during the process of valley deepening, similar to fluvial terraces. The alluvium fills of the studied caves in the Tarascon-sur-Ariège area, in the transition zone between the upper range and the piedmont, therefore enable the reconstruction of the geodynamic evolution of the Ariège River valley. All studied caves are developed on at least eight levels. Based on burial durations determined by 26Al/10Be and 10Be/21Ne terrestrial cosmogenic nuclide dating of samples from epiphreatic levels, our results indicate Langhian to Messinian (~13–5 Ma) incision rates averaging 48 m Myr−1. However, the obtained record does not allow us to accurately retrace the Pliocene evolution of the area due to the lack of known caves at corresponding levels. Moreover, raised local base levels during glacial phases both make the record more complex and call into question the methodological approach in terms of potential internal sediment remobilization and mixing related to implied re-flooding periods. •We identify eight regional cave levels in a Neogene valley in the eastern Pyrenees.•26Al/10Be, 10Be/21Ne burial durations obtained for intrakarstic alluvium.•Langhian-Messinian valley incision rates were ~48 m Myr−1.•Palaeodenudation rates increased by one order of magnitude since the Miocene.•Cave re-flooding events preclude a post-Pliocene reconstruction of the Ariège valley.