Boating south into Costa Rica begins with a visit to the migración office, located on the calle principal in San Carlos [1], on the waterfront near the park with a line that forms before 7 a.m. The office is open 8:30 a.m.–6 p.m. daily.
There are usually three or four boats to Los Chiles, starting at 10:30 a.m. The hour-long chug up the Rio Frío to Los Chiles, Costa Rica costs about $10 each way. To enter Nicaragua costs $7.
Once in Los Chiles, Costa Rica Migración is located 200 meters up the road from the dock, where you must get stamped. Daily direct buses depart for the five-hour trip to San José, about $8. Boats leave Los Chiles to San Carlos throughout the day (or, when there aren’t enough people, not at all, forcing you to spend the night in Costa Rica).
Note: Be aware that a second town by the name of Los Chiles is about two hours northeast of San Carlos, in Nicaragua. Be sure to distinguish between the two when asking for directions.
Links:
[1] http://www.moon.com/destinations/nicaragua/rio-san-juan/san-carlos