Larry and Jo,
If you all are starting from the Jax area, there are some really great suggestions from the Brats above. Toby and I completed an 11 day trip in May beginning on Lake Harney west of Mims Florida. We traveled north to Jax, up the ICW to Jekyll Island and then back south on the ICW to our home on Merritt Island, Fl. In May, that was about as far south as we could start our trip based on the available water depth at that time of the year. Lake Harney begins what is considered the middle section of the River. We would have started farther south if the water had permitted. Our county has now gotten up to the average rain level for this time of the year, so there is more water to run on now.
We traveled extensively on the River south of Lake Harney for about 4 years in a Lowe 14' aluminum boat with a 30 HP Johnson before we got our 22' Dory last June. But even in that boat, water depth was a seasonal factor in being able to get off the main channel and explore the back waters. One of the 3 main tributaries of the St. John's is just south of Lake Harney. The Econlockhatchee River flows in from the west about 1-2 miles south of Lake Harney and is navigable for quite a few miles back towards it's headwaters near Orlando. A really beautiful and primitive river with only 2-3 houses/cabins along it's banks. Also good fishing. Many folks kayak this river because it is so beautiful and relatively free of larger boats. The major lakes south of Lake Harney in order are Puzzle Lake, Lake Poinsett, Lake Winder, a dam and then Lake Washington west of Melbourne, FL.
Check out our album for St. John's River Mini Loop to see what the river looks like in the Lake Harney area. The Econlockhatchee is about 1 mile south of the bridge that you will see in the first picture and the cattle along the River is just after we moved out of Lake Harney into the River.
PM me if you want information about any specific lakes or areas in that section of the river. We have many photos that we have not posted in our album. We made another trip between Christmas and New Years and have several pictures of that trip that were never made into an album. We hooked up with Captain D on that trip in the Hontoon Island area for a cold one.
Tad