Episodic events of flood deposit in coastal environments are characterized by deposition of large quantities of sediment containing reactive organic matter within short periods of time. While steady-state modelling is common in sediment biogeochemical modelling, the inclusion of these events in current early diagenesis models has yet to be demonstrated. We adapted an existing model of early diagenetic processes to include the ability to mimic an immediate organic carbon deposition. The new model version (FESDIA) written in Fortran and R programming language was able to reproduce the basic trends from field sediment porewater data affected by the November 2008 flood event in the Rhône River prodelta. Simulation experiments on two end-member scenarios of sediment characteristics dictated by field observation (1–high thickness deposit, with low TOC (total organic carbon) and 2–low thickness, with high TOC), reveal contrasting evolutions of post-depositional profiles. A first-order approximation of the differences between subsequent profiles was used to characterize the timing of recovery (i.e. relaxation time) from this alteration. Our results indicate a longer relaxation time of approximately 4 months for and 5 months for DIC (dissolved inorganic carbon) in the first scenario, and less than 3 months for the second scenario which agreed with timescale observed in the field. A sensitivity analysis across a spectrum of these end-member cases for the organic carbon content (described as the enrichment factor α) and for sediment thickness indicates that the relaxation time for oxygen, sulfate, and DIC decreases with increasing organic enrichment for a sediment deposition that is less than 5 cm. However, for larger deposits (>14 cm), the relaxation time for oxygen, sulfate, and DIC increases with α. This can be related to the depth-dependent availability of oxidant and the diffusion of species. This study emphasizes the significance of these sediment characteristics in determining the sediment's short-term response in the presence of an episodic event. Furthermore, the model described here provides a useful tool to better understand the magnitude and dynamics of flooding event on biogeochemical reactions on the seafloor.