It used to be the San Diego kayak club paddled from Mission Bay (either Aqua Adventures or one of lagoons on the North side) to Shelter Island about 3 times a year, setting up a car shuttle. The club is more loosely organized now but I think the webpage is still active and you can get on the facebook and email list.
If you want a little more adventure on a low surf day you can launch from the Sunset Cliffs area, but this requires scrambling over boulders and ability to land on rocks (usually by bailing out, and swimming it in) and get your kayak back up the stairs or bluff, so not for the beginner, and best with a small plastic craft.
Deck Rigging Gear
Cartop Kayak Carriers
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