You have lots of choices from there. In Marion County proper (Ocala's county) you have the Rainbow River. The headwaters is a state park, and while there's a swimming area, you cannot remove anything from there. There are places downriver where you can rent canoes and put in and then explore on your own.
Ichetucknee Springs State Park - this one is about 1.5-2 hours away from the Ocala area. It's a spring fed river that is beautiful. In the summertime it's wall to wall people tubing and canoeing, this time of year, you will have it to yourself, except for an otter or two perhaps. Again, a state park and you cannot remove anything from here. Two cars would be nice so one can be left at the take out while the other goes to the put in. You're not allowed any food or drink inside the canoe while on state property.
Santa Fe River - makes the northwestern boundary of Alachua County (county immediately north of Marion). This time of year, there may not be as much aquatic life due to the cooler weather.
Withlacoochee River - never been there, but I think it's SW of the Ocala area. Ocklawaha River, just east of Ocala, but its dammed up near there, again not been there. Silver River (Silver Springs)- another major spring fed river just E of Ocala - headwaters is an attraction, but I'm sure you can find a place downstream somewhere to put in a canoe. Juniper Springs and Juniper Springs run in the Ocala national forest.
There's a sampler for you.
You can go on the Florida State Parks web site for other places which might interest you.