I was finally able to make it down there for a couple of days of Bay Fishing.. Really unique fishery they have there. Lots of different speicies to catch inside both San Diego and Mission Bay. I only fished San Diego bay both from a friends boat in the mornings and beat the banks by foot in several places both afternoons. Shore fishing was as good as the boat fishing but access takes some effort if your not familiar with the area.
Although lot's of room to fish on the water, you won't usually find the same solitude when shore fishing with a good majority of the bay developed. Non the less I had a great time both on and off the water and will be back in warmer months to do it again. Lots of flies worked but small, dark baitfish bugs seemed to get eaten more often than not. Bay and a few Sand Bass were at most stops both by boat and foot, as were juvinal Halibut on the fly on some of the flats. Other incidental fish were Jack Smelt, Macs and White Croakers (king fish in Nor Cal)
The Bonefish were hunkered down with the winter temps and we never ran accross any. My friend tells me he is able to target them with flies by blind casting with good success and they are getting bigger and more numerous.
Anyway, they hit the weather lottery there year round and if you havn't been, head down and give it a go. I had a blast! Good inshore Saltwater fishing and tons of places to stay walking distance from fish. Bob was a blast to fish with and knows the bay well. You can reach him at www.enlamosco.com