Modeling sediment transport and salt stratification in river estuaries: a case study of the Magdalena River, Colombia

• Numerical model adapted to assess hydrodynamics, sediment transport, and salinity in Magdalena estuary. • Low-flow and sea-level rise promote salt wedge intrusion up to 11 km inland. • Sediment plume patterns effectively reproduced and validated using Sentinel-2 imagery, indicating consistent model response. • Coastal infrastructure shapes magnitude and distribution of sediment deposition across estuary. This study presents a high-resolution three-dimensional numerical simulation of the hydrodynamics, salinity stratification, and sediment transport at the mouth of the Magdalena River, Colombia, using the EFDC + Explorer model. Field measurements and Sentinel-2 satellite imagery were used to calibrate and validate the model, showing high accuracy in reproducing salinity profiles (KGE > 0.7) and suspended sediment dynamics, including the formation of the estuarine turbidity maximum (ETM). Scenario simulations revealed that river discharge is the primary driver of sediment transport and salt wedge intrusion. At the same time, the influence of coastal infrastructure, such as the Western Breakwater, becomes significant under low-flow conditions. Under historical minimum discharge combined with a sea level rise of 1.2 m, the salt wedge extended up to 11 km inland, highlighting the vulnerability of the estuary to climate change. Morphodynamic simulations showed that high flows without the breakwater intensify sediment mobility and deposition near the mouth. The presence and configuration of the breakwater modulate both sediment dispersion and saline intrusion, with implications for navigability, coastal infrastructure, and estuarine ecosystem resilience. These findings provide a transferable modeling framework for other sediment-rich, microtidal tropical deltas facing similar climatic and anthropogenic pressures.