This study analyzed the hydrodynamic structure of the estuary and plume of a large, tropical, and strongly-stratified river, the Magdalena. The Magdalena River is the largest source of fresh water and sediment of the Caribbean Sea and drastically impacts the morphodynamics and ecosystems along the Colombian coast. The analyses are based on the results of a calibrated and validated numerical model. Three scenarios of low, mid, and high freshwater discharge were analyzed to consider the seasonal variability of the mixing processes. The relative importance of three mixing mechanisms in the system is investigated, and the estuary and plume are subdivided into sectors depending on the dominant hydrodynamic processes at each sector. The results show that mixing in this system is mainly controlled by turbulence at the pycnocline, especially at the lift-off point in the transition between the estuary and the plume's near-field. A hydraulic jump occurs in the transition between the near- and mid-fields of the plume, but the mixing produced here is comparatively low since the plume has been mostly diluted already in the estuary and the near-field. During low and mid discharge scenarios, saline intrusion in the river channel forms a strongly stratified estuary where bottom propagated turbulence generates instabilities producing minor mixing. Meanwhile, the saltwater is flushed out of the river during the high discharge scenario, and pycnocline instabilities produce mixing at least one order of magnitude larger than during low discharge conditions. Coriolis acceleration does not seem to be a relevant driver of the plume behavior, despite the larger extension of the plume during high discharges, given the low latitude of the system.