At the land-sea interface, the benthic carbon cycle is strongly influenced by the export of terrigenous particulate material across the river-ocean continuum. Episodic flood events delivering massive sedimentary materials can occur, but their short-term impact on carbon cycling is poorly understood. In this paper, we use a coupled data-model approach to estimate the temporal variations of sediment-water fluxes, biogeochemical pathways and their reaction rates during these abrupt phenomena. We studied one episodic depositional event in the vicinity of the Rhône River mouth (NW Mediterranean Sea) during the fall-winter of 2021-2022. The distribution of dissolved inorganic carbon (DIC), sulfate (SO₄^2-) and methane (CH₄) were measured in sediment porewater collected every 2 weeks before and after the deposition of a 25 cm sediment layer during the main winter flood event. Significant changes in the distribution of DIC, SO₄^2- and CH₄, concentrations were observed in the sediment porewaters. The use of an early diagenetic model (FESDIA) to calculate biogeochemical reaction rates and fluxes revealed that this type of flooding event can increase the total organic carbon mineralization rate in the sediment by 75% a few days after deposition, essentially by increasing the sulfate reduction contribution to total mineralization relative to non-flood depositional period. It predicts a short-term decrease of the DIC flux out of the sediment from 100 to 55 mmol m^-2 d^-1 after the deposition of the new sediment layer with a longer-term increase by 4%, therefore implying an initial internal storage of DIC in the newly deposited layer and a slow release over relaxation of the system. Furthermore, examination of the stoichiometric ratios of DIC and SO₄^2- as well as model output over this five-months window shows a decoupling between the two modes of sulfate reduction following the deposition - organoclastic sulfate reduction (OSR) intensified in the newly deposited layer below the sediment surface, whereas anaerobic oxidation of methane (AOM) intensified at depth below the former buried surface. This depth-wise bifurcation of both pathways of sulfate reduction in the sediment column is clearly related to the deepening of the sulfate-methane transition zone (SMTZ) by 25 cm after the flood deposition. Our findings highlight the significance of short-term transient biogeochemical processes at the seafloor and provide new insights on the benthic carbon cycle in the coastal ocean.