Mangrove seedling establishment is crucial to the long-term development of mangrove forests. This study incorporates a process-based approach for seedling establishment in a process-based hydrodynamic model. The biophysical model is used to simulate seedling establishment in the Firth of Thames estuary (New Zealand). The results are compared to a random seedling establishment approach that has been often-used in long-term mangrove forest development models. While small differences were observed in terms of the seaward extent of seedling establishment, larger differences were found for the patchiness and density of the establishing seedlings. The results of the process-based approach showed a more localized pattern of seedling establishment, in line with field observations in the Firth of Thames. This pattern was opposed to the more spatially uniform establishment patterns predicted with the random establishment approach. These differences reveal that the implemented seedling establishment approach may affect long-term mangrove forest development models. Moreover, the process-based approach is more easily setup and calibrated with physical parameters that can be measured in the field.