Mainland Bohol is oval-shaped, having a gentle, rolling terrain. Bohol's mountainous interior is home to rare and endangered flora and fauna. At certain points, hills drop steeply to the coast from a maximum elevation of 870 meters (2,850 ft.) above sea level. The interior uplands are fit for agro-forestry and high value agricultural production. The central and northern lowlands have also fertile grounds and abundant water supply. Over a hundred caves have been identified, the biggest of which is found in the eastern part, which makes Bohol ideal for spelunking adventures.

Hills dominate the island of Bohol. Two ranges run roughly parallel on the northwest and the southeast. An interior plateau is dominated by limestone hills. In Carmen, Batuan and Sagbayan, these hills form near perfect cones in great numbers and are collectively referred to as the Chocolate Hills. The Chocolate Hills in Carmen, Bohol are considered one of Philippine's natural wonders and Bohol is often referred to as the Jewel of the Philippines. They are hills made of limestone left over from coral reefs during the ice age when the island was submerged. They turn brown during the summer, hence their name.

White sandy beaches dot the coast of the island. The sand is often of such high quality that it is exported to other beaches in the world. The most well known of these beaches are in Panglao Island, and there, numerous islets have similar, yet untouched and pristine beaches.

There are four main rivers that run through Bohol with Loboc River being the most famous for its river cruises, running from the center of the island to the southeastern coast. The largest, Inabanga River, runs in the northwestern part of the province. The Abatan River in the southwest, and Ipil River in the north.

Numerous waterfalls and caves are scattered across the island, including the beautiful Mag-aso falls in Antequera. Mag-Aso means smoke in the native tongue. The water is cool and often creates a mist in humid mornings which can hide the falls.

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