The sedimentary record of the Paleocene–Eocene Thermal Maximum (PETM, ca. 56 Ma) allows the study of feedback mechanisms over the entire duration of a climatic event, from carbon release to the subsequent recovery phase. Clay sedimentation increase in the oceans during the PETM is linked to enhanced terrestrial erosion. Fluvial channel mobility has been invoked to explain this increase in fine sediment export based on more frequent transitional avulsions. In this study, we test whether the reworking of Microcodium (prismatic calcite concretions) from the floodplain to marine environments can serve to fingerprint floodplain reworking due to channel mobility. We quantified the abundance of floodplain-sourced Microcodium grains reworked in fluvial to marine sandstones pre-dating and coeval to the PETM in the Southern Pyrenees (Tremp Basin, Spain). Laser ablation–inductively coupled plasma–mass spectrometry U-Pb ages on calcite confirm the Thanetian age of the Microcodium grains. Our data show a four-fold increase in the export of floodplain sediments to the marine domain during the PETM. Moreover, we show that this is predominantly due to enhanced channel mobility, reworking channel banks and interfluves, with increased erosion in the hinterland as a secondary factor. This increase in floodplain reworking would correspond to an increase in biospheric carbon burial flux by a factor of 2.2. Therefore, enhanced channel mobility and fine-grain sediment transport to the oceans during a climatic perturbation such as the PETM may constitute an important negative feedback mechanism.