Sediment transport modelling in estuarine environments, characterised by cohesive and non-cohesive sediment mixtures, has to consider a time variation of erodibility due to consolidation. Generally, validated by settling column experiments, mud consolidation is now fairly well simulated; however, numerical models still have difficulty to simulate accurately the sedimentation and consolidation of mixed sediments for a wide range of initial conditions. This is partly due to the difficulty to formulate the contribution of sand in the hindered settling regime when segregation does not clearly occur. Based on extensive settling experiments with mud-sand mixtures, the objective of this study was to improve the numerical modelling of mixed-sediment consolidation by focusing on segregation processes. We used constitutive relationships following the fractal theory associated with a new segregation formulation based on the relative mud concentration. Using specific sets of parameters calibrated for each test—with different initial sediment concentration and sand content—the model achieved excellent prediction skills for simulating sediment height evolutions and concentration vertical profiles. It highlighted the model capacity to simulate properly the segregation occurrence for mud-sand mixtures characterised by a wide range of initial conditions. Nevertheless, calibration parameters varied significantly, as the fractal number ranged from 2.64 to 2.77. This study investigated the relevance of using a common set of parameters, which is generally required for 3D sediment transport modelling. Simulations were less accurate but remained satisfactory in an operational approach. Finally, a specific formulation for natural estuarine environments was proposed, simulating correctly the sedimentation-consolidation processes of mud-sand mixtures through 3D sediment transport modelling.