AbstractThe salinity structure in the Magdalena River estuary results from a massive river discharge and a micro-tidal regime over a narrow-deep channel. Both environmental forcings are analyzed here to assess their effects on the temporal and spatial variability of the estuarine system. We investigated long-term (seasonal to interannual) and short-term (diurnal) changes in salinity structure and circulation through in situ measurements and a 3D hydrodynamic model ensemble (21 model runs). The measurements cover low (below 10th percentile) and mean river discharge conditions. Results show that the Magdalena River estuary (MRE) behaves as a strongly stratified system during the dry season (February to April) and as a vertically homogeneous one during the wet and transitional seasons when the river plume exhibits a lift-off regime at the mouth. A river discharge threshold has been found for the estuary to lift-off regime transition, corresponding to the 30th percentile (5200 m3/s). At the seasonal scale, the salinity intrusion length in the MRE shows more reactivity to river discharge variability than other reported strongly stratified estuaries; it is reflected in the scaling factor $$n$$ n in the relationship $$L\sim {Q}^{-n}$$ L ∼ Q - n . A $$n$$ n value of 3.9 is the best fit for the MRE; nevertheless, it follows the Schijf and Schönfeld theoretical model solution for a prismatic flat configuration. Micro tides modulate the salinity intrusion on the diurnal cycle with a more significant effect on salinity intrusion and water exchange than previously reported, particularly during low discharge conditions. The findings from measurements and model scenarios for the MRE can be broadly applied and stand for an exemplary tropical, micro-tidal, anthropogenic intervened system.