In November 2008 we went from Tortuguero to San Juan del Norte (Nic) on a scheduled river boat that ran the Rio San Juan to Trinidad and then up the Rio Sarapiqui up to Puerto Viejo de Sarapiqui. It embarked from the canal side Pricessa Hotel. We got off at the first boarder point after leaving the canals, disembarking on the Nica side after checking in on the DR side, This leg of the trip took about 1 1/2 hours. The panga operators co-ordinated the arrival so that they were there at the same time as the east bound San Carlos -> San Juan del Norte panga. After paying a $10 border fee we had zero wait time and embarked on on the downriver side of the trip. We arrived in SJN about an hour later as we were on the fast panga (there is a fast & slow boat on the same day). We stayed with Edgar Colson at his cabinas on the north end of SJN and and an interesting few days. He is a great cook and wonderful man.
The border crossing is not a sanctioned one, though it is used by locals frequently and no one seemed to think what we were doing particularly unusual.. Our entry was by permit and allowed us to stay three days and required that we leave Nicaragua by the Rio San Juan after that. To do so we caught the west bound scheduled (fast) panga to San Carlos. When it got to the point where the river enters Nica territory not shared with DR, we had to get off and transfer to the DR side of the river. This leg of the trip took about 2 1/2 hours. It is the place where the Rio Sarapiqui enters the Rio San Juan and is called Trinidad. There is a small hotel there and they have an arrangement with the two border stations to pick up wayfarers. We stayed there 18 hours and in the morning caught the local panga down to Puerto Viejo de Sarapiqui (1 1/2 hrs). We could have hired a water taxi to to the trip on arrival, but they wanted over $100 for the trip. The hotel was OK and the food satisfactory.
This was an interesting adventure. We felt safe at all times though we were the only non-locals on the boats. To their credit the operators of the first panga managed to return a camera lens I left on their boat at the border. This had to be co-ordinated between two different panga boat companies, the border people and Edgar Colson. No one asked for a reward. This part of Nicaragua is not one seen by many. The flora and fauna here is as interesting as that on the DR side of the river, and much less observed. It has great historical significance and many interesting arteifacts from its colonial (British) history, as well as the more recent Contra affair. Don't be surprised if you pick up more English than Spanish in the locals conversations.