The Blackwater River Canoe Trail, combined with the Mud Bay loop, make for a great trip. I rented a Wilderness Systems 120 day kayak from Saltwater Sports in Naples.(239) 417-2200. The whole 13.5 mile trip probably went about 15 miles for me, given that finding the way through to the stream headed to Mud Bay is difficult. It took me all day.
The Blackwater River is solid mangrove lined all the way to the bay. It took me about 2 hours to cover the whole river. I paddled solid and took few breaks.
The outlet to the west and up to Mud Bay is not obvious. I asked two fishermen and only one of them had any idea. While the Blackwater river channel is well marked, the channel to Mud Bay is not marked at all.
Also, the ranger "warned me" about how difficult it was to find the outlet on the northern side of Mud Bay. The warning made it more difficult. I thought it was going to be a mangrove tunnel situation like the Turner River and as a result tried to spots that ultimately proved not to be right. The connection to the Blackwater is easy and obvious once located. It it not a mangrove forest situation.
Wildlife was plentiful. Alligators near the top of Blackwater. Numberous Ibis, Kingfisher, Osprey, Heron, and Egrets. Mud Bay is particularly fascinating. I was there near high tide, so it was too deep for the birds to stand in the flats. As a result the trees were filled and the birds were startled easily. When the flocking birds, egret, heron or ibis were startled by my presence, they flew off together forming a large mass in the low sky. It seemed like Africa at times due to the number of birds and remoteness of the bay.
I highly recommend this trip for strong paddlers with a good sense of direction.