The Suwannee is beautiful and still relatively unspoiled "old Florida." But, like the rest of the rivers around Florida's Big Bend, it's shoaly and can surprise you with limestone outcroppings, seldom charted. I know folks with small outboard-powered jonboats who have torn up props and lower units.
Along with several of the area rivers (Chassahowitzka, Withlacoochee, Waccasassa, Econfina, St. Marks, etc.), the Suwannee is kind of magical. i have cautiously explored them all in my trailerable power cat or by canoe and kayak. There used to be a houseboat rental livery at the Gateway Marina in Suwannee - the boats were a bit scuffed up, but I'd risk their bottoms and running gear before my own.