If you have just 1 day…
Pick up doughnuts (spiced chocolate or maple-glazed bacon apple) and Ritual Roasters coffee at the Dynamo Donuts kiosk on the Marina Green (dynamodonut.com).
Take an early boat to Alcatraz and spend a couple of hours exploring. If you couldn’t get tickets to Alcatraz, drive to Muir Woods instead. (You may want to leave your car in Mill Valley and take the free shuttle.)
Head to the Presidio. Check out the Society of California Pioneers, the Walt Disney Family Museum, and the Main Post Goldsworthy works. Or if you’d rather spend your time outside, hike the loop linking Lovers’ Lane, El Polin Spring, and Inspiration Point (where you’ll spot Spire).
Have lunch at Commissary or Arguello, Traci Des Jardins’ two Main Post restaurants.
Rent a bike at Sports Basement and pedal over to Fort Point, or up to the Golden Gate Bridge Plaza—trust us, the view’s just as good from this end, so don’t worry if you don’t have time to ride over the bridge.
If you’re ambitious, you could ride (or drive) over to Lands End, via Sea Cliff and Lincoln Park. Walk down to the remains of the Sutro Baths, which face Seal Rock (seabird central), or hike the Lands End trail.
Head east to Fort Mason for drinks at The Interval bar, and dinner at Greens (the views at sunset are amazing).
And if you have 2 more days…
You could spend all day hiking around and exploring the Marin Headlands, starting with Hawk Hill at dawn to watch the sun come up over the city. Knock off Muir Woods early in the day, to minimize the crowds—unless the weather is promising to be hot. In that case, save the redwoods for afternoon, when the deep shade will be most welcome. Try to include a rehydration stop at the Pelican Inn, in Muir Beach. End the day with dinner at Murray Circle, at the Cavallo Point Lodge. You could even fit in a massage at the hotel’s spa, if your legs are complaining.
The western beaches are on the agenda today: starting in the south in Pacifica, with a walk south along the sea wall from the town pier. A seemingly endless flight of wooden stairs leads to the top of Mori Point—from there, look for whales passing by. (If the place looks vaguely familiar, you may be remembering it from the 1971 classic film Harold and Maude.)
Make your way north, stopping at Fort Funston for a near-wilderness beach experience (cliffs, waves, windswept trees), and then at Ocean Beach for the urban equivalent (surfers, joggers, and the Cliff House rising above the northern end). If you’ve made it to the Cliff House before sunset, have a cocktail there and watch the sun sink into the Pacific. As night falls, bonfires may start to appear in the eight park-sanctioned fire rings down on the beach.
Have dinner at Outerlands, on Judah—the tables outside are reserved for walk-ins. (You might need to keep your sweater or coat on, but hey, you didn’t need a reservation.)