Propagule dispersal has generally been recognized as a vital factor affecting the spatial structure of tropical forest plants. However, available research shows that this hypothesis does not apply to mangrove species the propagules of which are dispersed by water. Due to the lack of comprehensive and quantitative information as well as the high spatio-temporal heterogeneity of the mangrove environment, the exact factors affecting the spatial structure of mangrove forests are poorly understood. To assess this, we selected a mangrove estuary with high mangrove species richness that experiences great changes in water salinity. After investigating the zonation of mature mangrove individuals across tides and the estuary, we measured the size and initial specific gravity of the propagules and then selected the eight most common species from which to observe the changes in specific gravity, buoyancy, and root initiation during dispersal at different sites with different water salinity regimes. The relationships among distribution patterns, propagule establishment, and dispersal behavior were investigated. We found that mangrove propagule dispersal is not a passively buoyant process controlled by water currents. During dispersal, mangrove propagules can actively adjust their specific gravity and root initiation. The dynamic specific gravity of the propagules was negatively related to propagule buoyancy and surface elevation. The differences in propagule specific gravity corroborated the distribution patterns of the species across the intertidal zone and estuary. Mangrove zonation on both the intertidal and estuarine scale can be explained by the tidal sorting hypothesis, as zonation is controlled by the tidal sorting of the propagules according to buoyancy and by the differential ability of the propagules to establish in the intertidal zones. The results add new understanding of observed mangrove species zonation and should inform conservation managers when restoring mangroves or evaluating the potential impacts of global change and anthropogenic disturbances that might alter the hydrology, including the water salinity regime.