Central America is a land of long coastlines and many rivers so naturally people travel by boat. In fact this was an early form of transportation into the interior because the dense hilly jungle is impenetrable, especially to outsiders.
Small boats, usually able to carry 10-12 people and their luggage frequent the navigable waters of the Caribbean and the rivers. They are more expensive than buses but often run where no bus route exists. Plus the views are great, and it's all part of the fun. There is also a chance to see wildlife, I saw hundreds of birds, including a toucan, as well as a manatee.
My personal experience comes from my time spent living and working at a hostel in Livingston, a small fishing town on the Caribbean Cost. It is only accessible by boat and I did a lot of back and forth. First I took a boat to Livingston from Punta Gorda, the left on one up El Rio Dulce to Rio Dulce town. Later I came back on a boat from Porto Barrios, and continued on back to Belize. It is also possible to take a boat to to Honduras, but should be noted that taking boats internationally are more expensive just as buses are.
The boats in and out of Livingston leave daily, but sometimes only once a day. The place where you are staying can reserve you a spot, usually by calling the boat captain. If you have a early morning boat ride out of the country make sure you square away your exit stamp and fee the day before.
Charter boats can also be hired to take you out to a private beach, to go spear fishing or snorkeling, or may be necessary to access some rain forest eco lodges.
Boats on the Ocean can be very choppy at times and depending on where your going can be several hours long. The seats are hard and uncomfortable, so if the seas look rough and you got a long way to go bring something to sit on or ask for a life jacket.