San Francisco waterfront can be an intimidating place to paddle for beginners/intermediates. There is a lot of fast boat traffic especially in the summer. There are two ferry terminals and a cruise ship terminal. The cityscape and the Bay bridge are amazing to look at but be careful of all the boat traffic around you. With that said, I've had many great experiences paddling around San Francisco and there are a lot of places to pull over if you are overwhelmed.
On January 9th, 2017, I paddled this stretch with plenty of rain and south wind. Storm-armageddon was back and I was a little concerned of my plan to paddle to Kirby Cove outside of the Golden Gate to camp there. Plus it was gonna be a sog-fest camping anyway. So I cut the plan short and paddled to Crissy Field instead. That turned out to be a great idea except the south wind along the northern city front was pushing me out into the bay and I had to fight pretty hard to stay close to the coast. Also since I paddled with the receding ebb, it gave me an extra push so all told it only took me a couple of hours.
Hazards: Where to start? In addition to what I mentioned on top of the page, you have to really understand tide currents and wind because now you're in serious open bay conditions. There are tankers, ferry boats, tug boats, speed boats, kite surfers, wind surfers, coast guards, surfers around Ford Point, etc etc... A missed calculation can put you at serious risk in terms of the ebb tide taking you out out of the Golden Gate. If you don't know how to negotiate any of the topics mentioned above, paddle with someone with experience or take a class. Just because you know how to paddle a board doesn't mean you know how to handle yourself in these conditions.
Put-in: Mission Creek or Mission Bay has several places where you can land. The Ramp (the restaurant) is a great place to land and have lunch. There's a public ramp at Bay View Boat Club which is nice (no bathroom), but you'll need to read the parking signs carefully due to the Giants schedule. Another great ramp is at the end of Mission Creek along Berry Street. There's a public bathroom there and also a boat house that belongs to UCSF. Parking is sparse though. On top of that, there's plans for the Warriors to move their stadium over to Mission Bay in the near future, so definitely forget about parking when that happens.
Take-out: Crissy Field is a great place for paddlers. The SFOCC (San Francisco Outrigger Canoe Club) has a location at Sports Basement parking lot and they have regular practices there. The beach is friendly to both kite/wind surfers and paddlers.