The short- to long-distance dispersal (SDD and LDD) of propagules is critical for the regeneration of mangrove forests. Mark–recapture experiments are considered to be a good tool for assessing such dispersal patterns. However, dense mangrove roots, exposed mudflats, shallow water, etc. often limit the number of recaptured propagules and their implication studies. Therefore, a combination of hydrodynamic and particle tracking models, together with a mark–recapture experiment, were applied to identify the dispersal behavior of Rhizophora mucronata Lamk. propagules in a coastal lagoon of Setiu Wetlands, Malaysia. The transport trajectories revealed that the dispersal of propagules is leptokurtic, with majority of them confined to very-short-distance dispersal (VSDD; 3–5 m) to SDD (1400 m). While higher obstacle density (e.g., mangrove roots) constrained the propagule dispersal, weaker tidal currents that coupled with less upstream discharge increased their retention time and settlement closer to the point of release. Under this scenario, the chances for propagules to exit from the lagoon mouth and their entry into the open waters for LDD are very limited. These results can explain the abundance of Rhizophora spp. in the northern sector of the Setiu Wetlands and be useful for species-level conservation/management.