There seems to be a lot of bad information on buses and how to get to/from San Juan del Sur, Nicaragua to La Fortuna, Costa Rica or vice-versa. I did this trip recently, and here’s the info on going from CR to NIC:
You want the 6am bus out of La Fortuna to El Tanque, which is just 1 town east and sits at a crossroads. The cost is less than $1 US.
Sit at the northeast corner of the crossroads. There is a small bus station/bench there. If unsure, ask the locals. At 6:50, a bus will pick you up going to Peñas Blancas, on the border of Nicaragua. Cost was 4,000 Colones. Travel time: almost 5 hours.
When the bus gets stuck in the huge line of traffic at the border crossing, ask if you can get out to see how long the line is. The driver will definitely say yes. Depending on how far back you are and how long it will take, you may just want to get out with your stuff and walk up to the border. The border crossing process is as follows:
1. You need to go to some shacks on the right side and pay the CR exit tax. Keep the receipt. The cost is $8 if you pay in Colones, $7 if you pay in US. Don’t ask. It just is.
2. Go across the line of traffic into a large gray building with windows. This is where you get your passport stamped. CHECK THE DATE. Lots of people had stamps with the wrong date and had to go back (including us) for a new stamp after arriving at the Nicaraguan side.
3. Continue walking in the original direction of travel and have your passport exit stamp/receipt checked at the Nicaraguan side.
4. Off to your left, go into a large tan/brown building for customs and passport control. Just inside the door, pay $1 US special fee. Assume it goes in a bribe/tip jar, because we weren’t allowed to question it.
5. Get in line for passport control and pay your $12 US entry fee to Nicaragua. US Dollars only – not even their home currency. If you don’t have the cash, they will let you leave your bags and passport behind, pass through to the ATM outside, then come back.
6. After getting your passport stamped, go to the customs inspection where they won’t even look at the screen while your bags go through.
On the outside, there are a zillion buses. Ask for the one to La Virgen and on to San Juan del Sur. It’s a common route, so they will know what you need. Ignore the taxis – it’s MUCH more expensive, no matter how much they lie to you about costs/time.
You’ll pay 25 Cordobas to La Virgen, get off, cross the road to sit on the right side of the fork in the road going the other direction, and wait there for the bus to San Juan del Sur. Don’t ride on to Rivas, if you don’t have to. It’s further, costs more, and just wastes your time. Travel time: 20-25min.
The bus going to San Juan del Sur will stop at your little roadside squat and pick you up for 17 Cordobas (hand baggage only) or 20 Cordobas (checked bags in the back). Travel time: 15-20min.
Expect a bunch of preachers to get on your buses in Nicaragua and yell about Jesus, until they are sweating. Don’t even try to engage them. They won’t stop or talk to you or do anything other than yell about Jesus.
Total travel time: 8 hours.
This post also has good info, with some pictures: http://travellentraversea.blogspot.mx/2012/12/costa-ricanicaragua-border-crossing.html