This study comprehensively analyzes the bedforms within the Magdalena River Estuary (MRE). Three sets of high-resolution bathymetric surveys conducted under varying climatological conditions were used to quantify the morphometry of the bedforms and analyze their evolution. Bedform dynamics were linked to hydrodynamic and sedimentologic processes previously documented for the MRE. The bedforms’ geometry of the MRE was compared with those of several estuaries and rivers using the Mahalanobis distance. The results show that during the low-discharge season, the salt wedge intrusion into the MRE inhibits the development of bedforms, resulting in a lower-stage plane bed. Meanwhile, larger dunes become predominant along the river channel when the salt wedge is flushed out of the estuary during high discharges. However, the symmetric shape of these dunes reflects the tidal influence on the river channel dynamics even during high discharges. Applying the Mahalanobis distance to the MRE and other fluvial and estuarine systems allowed us to systematically identify several geometric characteristics distinguishing between estuarine and fluvial bedforms. This research also proposes a nomenclature for standardizing geometric features in bedform studies.