I was born and raised in the bay area but now live in S. Florida. There are some good fly fishing opportunities to be had around the bay area. Here's a few recommendations....
- Salmon and steelhead fishing in the immediate area is tough. Some of the little coastal rivers used to be pretty good sometimes, but I have NO idea how they are fishing nowadays. The San Lorenzo River was and still is popular. I used to fish Pescadero Creek pretty often just upstream of the Hwy 1 bridge a few hundred yards. Lots of juvenile steelhead with an occasional 2-4lber. Seen some salmon caught too. Haven't been there in about 20 years, though!!!!
- Planted trout can be had at many bay area lakes, mostly in the East Bay region. Fly fishing for those should be feasible, especially from a watercraft. Coyote Creek just south of San Jose used to have good fishing for planted trout too....again, not sure how that is nowadays.
- Surf fishing can be good for perch and stripers. I never had the desire to fly fish the NorCal surf, but perch are abundant and stripers are caught regularly by guys in the know.
- Fly fishing the nearshore coastal waters for rockfish (aka rockcod) can be a ton of fun with flies, mainly in late spring through fall. You can rent a skiff or go out with a guide. Kind of like catching bass and they are generally very eager.
- Striped bass used to be my thing when I lived there. April through late October is generally best. I used to fish the south bay around San Mateo early in the season, then up north in the San Rafael region in fall. They like cleaner water, current, and structure like rocks/jetties, pilings, points/bends, slough entrances, etc but can also sometimes be out roaming on open flats too. A 7-9 weight rod, some type of sinking line (depending on depth), and some 1/0-3/0 chartreuse/white, yellow/white, or olive/white will catch fish all year. Try looking at areas from around the San Mateo Bridge on north...the far south end of the bay is often dirty and not really known for stripers. San Luis Reservoir and the adjacent O'Neill forebay about an hour from SJ are full of stripers (including some MONSTERS) but you'll need a boat or float tube for a legit shot at good fishing. Lots of ticks and rattlesnakes out there anyway.
- There's some good carp water in the south bay. My buddy has some secret spots that he wants to keep that way, but some of the lakes above San Jose/Morgan Hill are good for sight-casting to carp with flies on the flats. Again, beware of ticks and probably snakes too.
I have no idea where to shop for fly fishing gear in the area anymore other than the Bass Pro Shops in San Jose. The 2 fly shops I knew of and have been to are now out of business and probably got turned into tech company offices or $5,000/month apartments by now. lol.
Also, be sure to check out Demystifly.com which is TackleTour's sister site for fly fishing. I'm editor-in-chief over there and post new content each week.