This mangrove-blanketed area with its marine caverns is what put Río San Juan [1] on the tourism map to begin with, but since the huge media push of Playa Grande [2], it has fallen from its previous glory and suffers from lack of upkeep. However, tours are still given and can be quite a relaxing excursion.
Look for the Laguna Gri-Gri Tour Booth (tel. 809/589-2277) at the entrance to the lagoon, which is at the end of Calle Duarte. There you can arrange for a boat to take you for the two-hour ride through a kilometer of mangroves to Swallows Cave, where hundreds of the birds nest, onward for a swim in the Natural Swimming Pool. If you like, you can extend your trip for a two-hour layover at Playa Caletón. For a boatload of 3–7 people the trip will run you about US$30.
Links:
[1] http://www.moon.com/destinations/dominican-republic/the-north-coast/rio-san-juan
[2] http://www.moon.com/destinations/dominican-republic/the-north-coast/rio-san-juan/playa-grande