Density stratification plays a crucial role in estuarine hydrodynamics and material transport. In this study, we utilized a well-calibrated numerical model to investigate the stratification processes and underlying mechanisms in the dynamically wide Pearl River Estuary (PRE). In the upper estuary, longitudinal straining governs stratification, enhancing it during ebb tide and reducing it during flood tide. The Coriolis force becomes significant in the lower estuary due to the increased basin width, causing seaward freshwater to be confined to the West Shoal, where a pronounced transverse salinity gradient forms. Interacting with lateral current shear, density stratification is most pronounced in this region. The prevailing northeasterly wind creates a mixed layer near the surface, shifting stratification to the middle layer of the water column in the upper estuary. Wind stirring reduces stratification throughout the estuary. Under the wind’s influence, the seaward outflow is confined to a narrower region and shifts westward, resulting in the most apparent stratification occurring on the West Shoal of the PRE due to lateral straining. These findings on the evolution of freshwater pathways and their role in modulating density stratification have significant implications for other wide estuaries, such as Delaware Bay and the La Plata-Parana estuary.