Here's a quick look at where to anchor while in San Diego.
You need a permit in advance, apply online here.
A1- Playa Anchorage
Pros: Close to Downwind Marine / San Diego Marine exchange and many marine related service providers. Lots of restaurants within walking distance and shopping at Ralph's is about a 10 minute walk. Great wind protection and dead flat water.
Cons: Advance permit required, cut off to book is Thursday midnight, and the anchorage is limited to Fri-Sun night only.
No dinghy dock access except at Police docks. Sand beach is an easy landing, but security could be a problem after dark.
A5- Glorietta Bay
Cons: Permit required with max stay of 3 days. Vons grocery store is a pretty long walk.
A9- Cruisers Anchorage
Cons: Permit and special inspection required. Rolly, noisy and located in the middle of nowhere at the edge of the San Diego airport, security at dinghy dock is definitley an issue as are an abundance of panhandlers.
Mariners Basin, Mission Bay
Cons: Max stay 72 hours in any 7 day period. Sand beach is an easy landing, but security could be a problem after dark.
Mariners Basin with some storm clouds on the horizon.
San Diego Free Anchorage-
Pros: Free for all.
Cons: Outside bay and a true road-stead anchorage. Full of derelict boat(er)s. Under military runway flight path and a long rough dingy ride to anywhere.
If you want a mooring ball then it's just one call to San Diego Mooring Company who manages all moorings in San Diego Harbor, but it could be a wait.