Agatti is characterized by an extremely flat, low-lying topography, typical of coral atolls worldwide. There are no hills, mountains, valleys, or significant geological uplifts. The highest point on the island is a mere 3 to 4 meters above sea level.
The terrain consists entirely of coral sand and limestone debris accumulated over millennia. Its coastal areas are predominantly white sand beaches, transitioning quickly into shallow lagoons on the western side, while the eastern shore drops off more sharply into the deeper waters of the Arabian Sea. Because of this low elevation, Agatti is highly vulnerable to coastal erosion and the global threat of sea-level rise.