The Tagbilaran City Port handles more than 4,000 passengers per day. An average ship calls of 15 vessels per day from surrounding provinces like Cebu, Cagayan de Oro City, Dumaguete, Dipolog, Iligan City, Larena, Plaridel, Ozamiz City,and Manila are processed efficiently.

Fast ferry trips from Cebu reduces the travel time between Cebu and Bohol, reducing the travel time to only one hour and a half. Aside from the Tagbilaran Port, there are other ports around the province. The port in Jagna town serves as the province's gateway to Mindanao.

Bohol can also be reached through the minor ports located in Ubay, Tubigon, and Talibon.