If you own a kayak, you may launch at City Kayak space for free. South Beach Harbor designates a space also, but often there are changes due to construction, maintenance issues. Ask City Kayak for the latest information.
There is no fee to launch to access SF Bay or McCovey Cove. But, any foot traffic or floats are used by boaters, carts, and wheel chairs. Keep your kayaks and gear away from getting in other peoples' way.
If you bring own kayak, you will need to park elsewhere(street metered parking or paid lots).