My sister and I recently went chasing waterfalls as part of our Bohol backpacking trip. We took a van ride from the Dao Bus Terminal from near the Island Mall. The departure times can be a bit of an unknown as it will not leave until it is fully occupied; we were quite lucky and only had to wait for 20 minutes. Fares are 100/pax one way.
Bohol is a one off wonder that has it all- the sun, shimmering, crystal clear sea, soft sand and spotless beaches, a cornucopia of amazing historic heritage sites, and panoramic sensational scenery and if that isn't enough folks, you can do it all on a shoe string if you feel so inclined.