The only regular boat service is to Castillo from San Carlos. To truly explore the river and its tributaries, you need a private boat with guide, possibly arranged in San Carlos, but best arranged with the expert agencies in Managua who will provide English-speaking, qualified guides. Access to many tributaries is restricted, and you must show written permission from MARENA in Managua to get past the many checkpoints and soldiers. Needless to say, pack the strongest bug repellent you can find and wear clothes that easily dry.
Note: This information was accurate when it was published, but can change without notice. Please be sure to confirm all rates and details directly with the companies in question before planning your trip.