With several reservoirs and of course the coastline, San Diego is a great place for kayak touring. Kayaks can be found cheaply with careful shopping (found my first for $300 on Craigslist). Be sure to check on closures here, some of these reservoirs are only open a few days per week, or close completely for the winter.
AKA Carlsbad Lagoon. One of the only coastal lagoons that's open to kayakers. Don't get sucked into the $10 launch fee at the recreation site seen from the 5, there's a free place to launch if you're willing to carry your boat a short distance (update - Carlsbad Parks and Recreation sometimes has a tent setup to collect launch fees, so free launching is no longer certain).
A gigantic reservoir surrounded by mountains. When the water level is right, I've paddled under tree cover and seen lots of bird life just south of the launch ramp.
Launch from a parking lot near Centennial Park, then paddle across San Diego Bay to near downtown and the Midway.
Drive onto the sand just about anywhere on the island for an extremely easy launch into Mission Bay.
Another large reservoir with lots to explore. When the water level is high enough you can weave through Eucalyptus trees underneath the pedestrian bridge and 15 freeway.
A San Diego must. Launch on the beach and paddle over to the caves and seals. Hundreds of leopard sharks can be seen in shallow water when its warm out.
A small lake that can be explored in a few hours. Often very clear water, and sometimes turtles can be seen lounging on the reeds, especially when the water is low.
A very nice setting worthy of a visit. The size has shrunk drastically from what is shown on the map.
Upper Otay is off-limits, but Lower Otay would take several visits to see the whole thing. Passageways can be found through vegetation in the far east finger.
San Vicente As soon as it reopens!!
One of my favorite paddles when the water level is high. Lots of birds and places to beach your boat.
The below places are outside of San Diego, but if you find yourself with a kayak, I can't recommend them enough.
Hire these guys to drop you off at Norton's Landing (or set up a long car shuttle and start from Taylor Lake) and make your way back to Fisher's Landing. ~15 miles of relaxing and scenic river to cruise, with side passages through reeds into hidden lakes. Camp at Norton's, Taylor, or Picacho to make a weekend out of it.
Kayak to Paoha Island and set up camp. Billions of brine shrimp (yes, sea monkeys) in the water (and in your kayak), boiling water bubbling in Paoha Bay, the remains of an old tuberculosis resort, and paddling through tufa should keep you plenty interested. Don't forget to get a proper permit.
Yes, you may have to wade through rotting fish carcasses to get the kayak into deep enough water to paddle, but there's nothing quite like the Salton Sea. Paddle one way to a campground on the eastern shore where you can score a much-needed shower, and sit back and enjoy one of best sunsets you'll ever see, reflected against California's largest lake.