There are also day tours to the jungle rivers on the mainland. They are kayaking/canoe trips and I hear they are simply wonderful. I didn't try it, but I bet if you dig on the internet you'll find them. Try Excalibur Tours in San Pedro. Actually, if these tour places don't have what you want, it was my experience they will do their best to find it for you.
We stayed on the Macal River for part of our trip, and it was so breathtaking, I wish we had canoed and kayaked. Maybe when we go next year.