Independent long-distance kayak trip

I am not sure about the San Blas, but there is plenty of Bocas that is WAY off the beaten path. If you look on a map there are no roads for the Caribbean coast between Bocas and Colon. Check out this place, isla escudo de veraguas. As for rivers. There is rafting in the Chiriqui highlands outside of Boquete and I know there are a ton of rivers in the Bocas region that never sees any tourist at all. If you google it rigt I think you can find an article about some people that explored some rivers in Bocas. Also as a nice day trip, the Changuinola canal and the San San Pok wetlands are incredible and are home to Manatees.

Are you strictly looking at Panama or willing to look at other places in CA?
I agree the Bocas area would be great to paddle, everything from lot's of Islands and a bunch of rivers.
You have a folbot type of kayak?

Thank you so much for both your responses, great help!
Maliante, I like the idea of possibly starting in starting in Bocas, and heading down the coast toward Colon going through Isla Escudo de Veraguas which looks amazing! What does the coast look like, is it mailny Mangroves or are there actual beaches between Colon and Bocas? Also As far wind and current goes, would you know which direction would be best (Bocas to Colon, or Colon to Bocas)?
Hermosaje, no, actually I am open to any suggestions. Please let me know any other places you would recommend! As for my Kayak, it'S an sturdy inflatable one, I've used it on three expeditions (about 10 days each) down the Gambia River in Africa, in the PAlau Archipelago in the Pacific and in the Colombian Amazon. It's got a lot of drag (compared to a hard kayak), but it'S very convenient for travel.
Looking forward to hearing back, thanks!

I don't know what that part of the Caribbean is like. There was going to be a road leading from Santa Fe De Veraguas to the Caribbean but I don't think it is finished although you can accsess it by RIVER. It seems like it would take awhile to get to Colon but I Really don't know. You probably want to research how the sees are that time of year.

Well there are a couple of places you might look at, the Rio San Juan, from Lake Nicaragua to the coast and then take a fast boat back. There have been a to couple trip reports on kayaking the San Juan in the last couple of years on the TT. I've done the trip up the river, it's remote but not what I would call beautiful. To get to the more jungle places you need to get a mile or 2 into the tributaries, especially for more wildlife. Lot's of Croc's on the river and good fishing. It would be a fun 5-8 day adventure. Myabe a couple simple class 2.5 ripples.
The Solentiname Islands on the lake look fantastic as well.
Take a look at kevinberg53 trip report on Feb. 4, 2013.

The Rio Pacuare in Costa Rica is a beautiful pristine river, nice canyons and waterfalls. I've only floated it, but man the whole way I wished I had my yak and camping equipment. I would guess it's maybe 2-3 days to the coast if you took it very slow. I'm sure if you contacted the folks who run the rafting trips they could give you the basic logistics. At best there are some easy class 3 sections with large pools after each one. After the river you could paddle around the NP in Cahuita and down to Puerto Viejo and even Manzanillo.

Another great 8-10 day paddle is Isla Carmen in Baja Sur off Loreto. It's a remote huge island, no people whatsoever, excellent fishing, snorkeling and hiking, you'll be the only one around. Only drawback is no fresh water, my yak felt like barge the first few days, it's an absolutely beautiful place. The best time is March to April though. Something to keep in your back pocket for a future paddle.

Yeah I have both, folbot and hard side Necky. It's killer to fly into a place and put the folbot together and go off for day days, especially considering how much they charge for yak rentals.

THank you for all the great advice Hermosajoe, I'm going to take the time to look into the different options you mention. And yes I totally agree, having your own transportable mode of transport is like total freedom, I love it.

So after talking about it with my girlfriend and reading through a few websites, etc. the San Blas islands seem to attract us the most, however we cannot seem to find any information about the possibility of kayaking through the islands independently. Everything seems to be very controlled. Is it possible to visit the islands independently (by only paying the entry fee to the comarca and then kayaking around the islands by ourselves, camping on uninhabited islands, etc.)?

The short answer is no. Even on kayak tours there is a Kuna escort.
Maybe take a look at Belize. Check with the operators on Caye Caulker, sounds like what your looking for and less hassle.