The aforementioned journey can be undertaken as daytrips or even multiple-daytrips. However, it is also possible to kayak down the whole river, leaving from San Carlos and reaching the coast several days later. This requires a bit more planning and effort than kayaking only part of the river, but the experience will be certainly worth it.
The main difference when kayaking down the whole river is that more food and supplies should be brought along during the trip. This includes the baggage as well. Although food and drinks are available along the way during the first part of the trip, they are scarcer after El Castillo. It is therefore important to bring enough water, bread, snacks, and other necessities to take throughout the day. There are no shops between the stops, so lunch should always be brought along. Furthermore, remember there is no escape for the intense sun so bring enough water. After El Castillo, supplies can be restocked at Boca de San Carlos and at a shop just after the town of Sarapiqui. There are simple options to dine in both Boca de San Carlos and Sarapiqui.
The 200 km journey can take anything between 3 and 8 days, depending on the stops and speed of the paddlers. Very experienced paddlers can get in one day from San Carlos to El Castillo, on the second they they can reach Sarapiqui, and on the third day San Juan del Norte. Please note that this tempo requires an athletic condition.
People who are little experienced with kayaking but adventure-minded can certainly also undertake this journey. With a good guide and proper equipment, this is a beautiful and safe tour. Going at a slower pace, it would take one day to reach Sábalos. From here, it is probably best to go up to Bartola the next day if time is important. This is a good base to reach Boca de San Carlos the next day. On the fourth day, Sarapiqui can be reached. These paddlers would arrive in San Juan del Norte on the fifth day. However, making some more stops and staying at least one day in El Castillo to see the fortress is highly recommended.
Enthusiasts who like nature and adventure can easily spend 14 days in the Río San Juan region. Staying more than one night at interesting places like Sábalos, El Castillo and Bartola easily adds up, and San Juan del Norte is also an attraction by itself. It is generally not necessary to make reservations ahead when not in the peak season, but when visiting in July-August or December-January, then it is useful to plan ahead.
You can read more about kayak options at the San Juan River here.