The linkage between the salt wedge, tidal patterns, and the Magdalena River discharge is established by assessing the ensuing parameters: stratification (ϵ), buoyancy frequency (β), potential energy anomaly (φ), Richardson number by layers (RL), and bottom turbulent energy production (P). The salinity, temperature, density, and water velocity data utilized were derived from MOHID 3D, a previously tailored and validated model for the Magdalena River estuary. To grasp the dynamics of the river, a flow regime analysis was conducted during both the wet and dry climatic seasons of the Colombian Caribbean. The utilization of this model aimed to delineate the estuary’s spatial reach, considering flow rates spanning from 2000 to 6500 m3/s across two tidal cycles. This approach facilitates the prediction of the position, stability, and stratification degree of the salt front. Among the conclusions drawn, it is highlighted that: 1. The river flow serves as the principal conditioning agent for the system, inducing a strong estuary response to weather stations; 2. The extent of wedge intrusion and the river discharge exhibit a non-linear, inversely correlation; 3. Tidal waves cause differences of up to 1000 m in the horizontal extent of the wedge; 4. Widespread channel erosion occurs during the rainy season when the salt intrusion does not exceed 2 km; 5. Flocculation processes intensify during the transition between the dry and wet seasons; 6. The stability of the salt layering and the consolidation of the FSI–TMZ are contingent upon the geometric attributes of the channel.