Wetlands are essential for global biogeochemical cycles and ecosystem services, with the dynamics of soil organic carbon (SOC) serving as the critical regulatory mechanism for these processes. However, accurately modeling carbon dynamics in wetlands presents challenges due to their complexity. Traditional approaches often fail to capture spatial variations, long-range transport, and periodical flooding dynamics, leading to uncertainties in carbon flux predictions. To tackle these challenges, we introduce a novel extension of the fractional RothC model, integrating temporal fractional-order derivatives into spatial dimensions. This enhancement allows for the creation of a more adaptive tool for analyzing SOC dynamics. Our differential model incorporates Richardson–Richard’s equation for moisture fluxes, a diffusion–advection–reaction equation for fractional-order dynamics of SOC compounds, and a temperature transport equation. We examine the influence of diffusive movement and sediment moisture content on model solutions, as well as the impact of including advection terms. Finally, we validated the model on a restored wetland scenario at the Ebro Delta site, aiming to evaluate the effectiveness of flooding strategies in enhancing carbon sequestration and ecosystem resilience.