Mayabunder is located on the eastern coast of Middle Andaman Island, facing the Andaman Sea. The geography is characterized by dense, tropical evergreen forests and a highly indented coastline rich in mangrove ecosystems.
The region's geography plays a critical role in its ecology, providing a buffer against coastal erosion and offering a sanctuary for diverse marine and bird life. Offshore, several small uninhabited islands dot the seascape, including the locally famous Avis Island, known for its coconut plantations and coral reefs.