Rather than try to hit up as many places as possible, I’d recommend going to a few places and really enjoying yourself there. I’ve definitely been on trips where I wanted to get “as much” as possible but in the end have found it not very fulfulling and also very tiring. But maybe that’s just me.
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Thanks, good advice! I haven’t gone on enough trips to really say one way or another, though California’s a bit unique in that it’s both a biodiversity hotspot and most of the sites are accessible enough, so the act of missing one might be nagging at my conscience, but I’ll be sure to keep that in mind!
Currently leaning towards Muir Woods (maybe Henry Cowell too when returning from Monterey), Ring Mountain (same day as Muir Woods), Mt. Diablo, Pt. Reyes, Golden Gate NRA, Ano Nuevo, Fitzgerald Marine Reserve, and a visit to CalSci and MBARI. Possibly Tamalpais and a few more if I have time. Depends on how much my family wants to go to Yosemite though; if they insist, I’ll probably have to strike out a bunch of these.
(although I’m only truly free on 5 of 9 days, I’m still semi-free on all but one of the days, basically just meaning that I have to attend to family stuff by the evenings but will still be free during the mornings and afternoons)
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If 3-4 miles is too far, sometimes a few bulls used to hang out at another little beach near the visitor center. It won’t be as busy in May as during the winter.
So, Fitzgerald Marine reserve and Pillar Point are about 30-40 minutes from SF, depending on where you’re staying in the city.
Año Nuevo State Park is maybe 45 min. south from Pillar Point and Fitzgerald Marine Reserve.
There are some cool coastal places to visit right in the city, but I’m not very familiar with that.
You might consider taking a ferry from Sausalito and hiking Angel Island in the bay.
Ps… here is a pretty good tide chart. You can plug in your dates and see when the tides are high and low.
https://tides4fishing.com/us/california/pillar-point-harbor
I think you can change the location, too, for more precise timing.
I’m thinking about going to Fitzgerald on its own shortly after I arrive, just because that’s when it seems that the low tide will be at its lowest for the week that I’m at SF. Debating over whether to go to Ano Nuevo on its own/wrap it into the Fitzgerald trip and return to SF afterwards or wrap it into a 2-day Monterey trip, I’ll have to plan that out. Probably wouldn’t have time for Sausalito + Angel Island though.
Question, but are the Coulter Pines easily visible on Mt. Diablo, or do you have to go off-trail for them?
(Hangs head) 
I’ve never been to Mt Diablo. I’m sure Tony @tiwane and others can give you some great advice on that, though. There are dozens of places to visit in the East Bay.
Yosemite is about 4 hours from San Francisco, much more in traffic. You used to need reservations in advance there. Mariposa is a small outside the park, if you don’t t have accommodations in Yosemite itself. I’
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Here’s a map: https://www.inaturalist.org/observations?place_id=5586&subview=map&taxon_id=67330 Many are close to trails.
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Ah I see, no problem! Also, are there any places around San Francisco to easily spot sea lions?
Fisherman’s Wharf used to be loaded with them. 
Edit… sorry, I meant pier 39, I think.
There are usually a some are around Fitzgerald, pillar Point, and Santa Cruz wharf.
I’m only giving info on areas I’m sort of familiar with, but I’m sure others know where to see seals in the City and Marin County, Oakland and Berkeley.
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In case I did not mention, I 2nd what Tony @tiwane said about Pt Reyes. It is marvelous, though best to visit during the week, I think.
I am wiling away my time during a long day drive today on iNat. I’m tired of sitting in the car. My current perspective suggests: pick something closer to the city! Spend more time exploring, less time getting there. 
On that note, I suggest going with just five places (five available days). Monterey Bay is kinda far from the others – I don’t even really think of it as the Bay area. Point Reyes, Golden Gate Recreation Area, and Muir Woods are all very much North Bay, whereas Monterey Bay is further south than South Bay. You can see from this screenshot how close together those first three are, and that there are several other natural area reserves nearby, too:
With that said, Mt Diablo is good for a radical change of scene without going too far away from the others. That would be considered East Bay. For that matter, I got my lifer Coast Range Dudleya at the Skyline Wilderness Preserve in Napa, which is also in North Bay – take the River-to-Ridge trail that goes down toward Napa Valley College. If you’re looking to get lots of species, you don’t necessarily need to go to the most iconic or scenic places.
Just note you need a shuttle reservation for Muir Woods… Unless you’re up for a long hike: In that case, you can hike in from Mt. Tamalpais for free!
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I’ve been seeing some very nice wildflower pictures from the Tomales Point trail in Point Reyes National Seashore lately. Might be a good option. Abbott’s Lagoon and the Drake’s Estero trail are favorites, too. There’s a family of river otters near the lagoon, and if you’re lucky you can see bat rays and leopard sharks in the estero. Just get there early. Parking fills up fast.
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Sonoma Coast State Park is very nice if you want to go a little further north than Pt. Reyes. Bodega head is good for whale spotting, and I like watching the seals and sea lions by the mouth of the river at goat rock beach. Not to mention there’s lots of good restaurants in Bodega Bay. Fishetarian is one of my favorites. And Spud Point Crab Co. for really cheap crab sandwiches.
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Thanks! I’m thinking about visiting Monterey Bay primarily because visiting the aquarium has been a childhood dream of mine so I really want to visit it, even at the expense of visiting Pinnacles (same distance away) and getting my lifer California condor there. But thanks for the info!
I am thinking about getting a vehicle reservation for Muir Woods once I get a more concrete timeline for the trip, though I do admit, a hike up Mount Tamalpais does seem quite tantalizing given its apparent floral diversity; how long does it take?
Well, you will likely see wild seals and rafts of otters in the ocean right by the Monterey Bay Aquarium, as well as many shore birds. It is the best of the local aquariums, IMO.
But, if you turn out to be short of time for such a long drive (potential traffic at some points), there are 2 decent aquariums right in San Francisco.
- Steinhart Aquarium in Golden Gate Park
- Aquarium of the Bay at the wharf
It’s a long day hike if you want you go from Mt. Tam all the way to the Visitor’s Center in Muir Woods and back. It’s about 4.5 miles one way from the Rock Springs Picnic Area (which has no parking fee) to the Muir Woods Visitor’s Center, and there is a significant elevation difference, so going back uphill on the way back can be pretty strenuous. You can shorten it a little if you start at the Bootjack parking lot, but there is a fee to park there (probably less than it costs to get in on the Muir Woods side, though). The plus side is coming in from that direction, there are very few people until the last mile or so before the Visitor’s Center. The area immediately around the Muir Woods Visitor’s Center can be quite crowded. It’s much nicer where there aren’t so many people. You can always decide to cut the hike a little shorter and turn around before you get all the way to the bottom, too.
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https://www.birdandmoon.com/comic/naturalist-hike/
See above (originally posted in the topic, Nature Inspired Comics)
Are there any good places to find California quail out of the areas I’ve suggested? Are there any other specialty birds in the area? (aside from the condor, which I’ll probably have to pass on due to lack of time)
Also, I’ve just remembered that the vicinity of Monterey has some very unique relict plant habitats. Aside from the Lone Cypress, are there any other important plant habitats to see there, especially for endemic species?