Water erosion in upland riverine areas leads to sedimentation in the lowlands, which also affects certain habitats in the estuarine ecosystem. The alteration of the estuarine ecosystem has affected the shifting of mangrove habitat in Segara Anakan Lagoon (SAL). Heavy sedimentation has impacted this area as a result of complex natural and anthropogenic activities that are causing soil erosion in the Citanduy River’s upstream area. Sedimentation causes new land to emerge gradually, reducing water area. It had also altered the environment, particularly in the western part of the SAL. It is responsible for the degradation of critical habitats such as marine biota and mangrove forests. Monitoring is essential for providing policymakers and other stakeholders with an accurate picture of the situation when managing their area and its resources. With spatial-based information, users can easily understand a comprehensive picture of phenomena that occur in a specific area. This study used the LULCC (Land Use/Land Cover Change) model to predict a shift in the lagoon habitat. The model revealed that the change in landform has mostly contributed to the alteration of mangrove composition and its distribution in the study area. The sedimentation process has led to the development of new lands, creating a low-saline environment that fosters the growth of invasive plant species. Further, invasive plant species will replace mangrove forest in the majority of the lagoon water area. The model predicted that the lagoon’s water area would shrink by 57% over the next five decades.