Organized ferry and water-taxi service is available between Panama City and Isla Taboga and sometimes Contadora, and between the mainland and Isla Colón in Bocas del Toro province. Other than these services, boat transportation for travelers is generally more casual and arranged ad hoc.

Boats are the main means of regional transportation within the archipelagos of Bocas del Toro and Kuna Yala (San Blas Islands). They are also the main way to get around the densely forested parts of the Darién and mainland Bocas close to rivers, especially in the rainy season when the rivers are more easily navigable.

The Bocas archipelago is the only place with anything resembling scheduled, cheap, commercial boat transportation among the islands. Boat transportation everyplace else is usually a matter of tracking down a fisherman or enterprising local boat owner and negotiating a price for a tour or extended trip.

This can get expensive quickly. Tours are generally charged by the hour per group; the price for longer trips is based on distance, with gasoline the biggest expense. The price always includes the boat, a captain (and crew, if needed), and fuel. As always, agree on a price ahead of time.

Transportation is generally in exceptionally long wooden dugouts called piraguas, though fiberglass boats (botes) are also used in some places. Both come equipped with outboard motors. For long trips especially, check the horsepower of the motor, and ask if there’s a backup motor and life jackets (salvavidas).

Piraguas are actually the preferred form of transportation on the river. Long dugouts used on the ocean are similar, but they have higher sides and an angled prow to break the waves. Short dugouts called cayucos are powered by a single wooden paddle and are all too easy for inexperienced paddlers to flip; it’s unlikely you’ll find yourself in one except for a very short trip.

Chartered sailboats, fishing or diving trips, and other outdoor activities on more substantial boats are easy to come by, but they tend to be quite expensive.

It’s possible to take a partial or complete transit of the Panama Canal every Saturday via small vessel.