Mangrove forests provide important estuarine ecosystem services but are threatened by rising sea levels and anthropogenic impacts. Understanding the habitat characteristics required for mangrove growth is significant for mangrove restoration and integrated management. This study aims to build spatial habitat suitability index (HSI) models for Kandelia obovata mangrove trees. Biological and habitat-related environmental data were collected in the Wazwei and Guandu wetlands in northern Taiwan. We adopted inundation frequency, soil sorting coefficient, and water salinity as the key environmental factors to build HSI models. The dependent variable of these environmental factors was the mangrove biomass per unit area. Significant differences were found for the mangrove biomass on different substrata and shore elevations. The tidal creek had the lowest elevation, and mangrove areas were found at the highest elevations. The oxidization level of the substrate under mangrove forests was high, indicating that the root system of mangroves could carry oxygen into the soil and result in oxidation. Human activities were found to lead to the reduced growth conditions of mangroves. The validation of the HSI model, considering the inundation frequency and soil sorting coefficient, proved to be reliable, with an accuracy ranging from 78% to 90%. A better simulation was found after revising the model by incorporating the factor of water salinity. The model forecast of the mangrove responses to the sea-level rise indicated an increase in the inundation frequency and thus an induced shift and shrinkage of the mangrove area. The increased HSI values of the bare mudflat area demonstrate an option for the potential restoration of mangrove trees. Given the findings of this study, we concluded that mangroves could spread from estuaries to upstream areas due to rising sea levels and might be limited by humanmade impacts. Restoring degraded floodplains is suggested for mangrove habitat rehabilitation.