Where will you be staying, and how mobile will you be?

San Diego Zoo

We will probably rent a car.
We can probably walk a mile or so, stay on our feet one hour or so.

The zoo will take you more than an hour, and it’s pretty expensive for just that short amount of time. Museums are much cheaper and it’s quite nice there in Balboa Park. Of the beaches, Mission Beach has the most parking by Belmont Park, but it’s the most crowded beach. If beer is your jam there are over a hundred microbreweries in San Diego. Lots of good food too. Take in a Padres game; they actually don’t suck this year. Maybe take a boat ride in the harbor or the ocean. Deep sea fishing. Mexico. La Jolla. Del Mar Race track if you’re there in July. Old Town. The Presidio. The Mission. Go to a magic show. Lots of music. Take in a play at the Old Globe Theater. Lots of beaches—I mentioned Mission Beach above but there are lots more. Take a drive to the desert, although the wildflowers are probably over by now. Go to the Hotel Del Coronado and eat a $15 burger (it’s nice to walk around, though). Go to Point Loma and check out the Cabrillo National Monument. See the USS Midway Museum. Go to the Star of India. Sea World is there but I don’t do Sea World. Legoland up north.

Lyft and Uber are there so if you don’t want to rent a car, those are pretty easy.

Thank you, @Caravanfan!

I always think the cool thing to do in a new town is get on one of those hop on hop off rides. San Diego has one. Great way to get a look.

But, being familiar with San Diego here is my advice to tourists-

On the east side of the bay, there is a whole strip, the Embarcadero Marina area, that has restaurants and stuff. Its fun to walk there. As stated, you really should check out the USS Midway.

If you have a car drive over the Coronado bridge, a thrill ride in itself, and go down the causeway (Silver Strand Blvd, Cal 75) and check out my personal favorite-The Naval Amphibious Base. You can see training stuff on both sides of the road. Farther south is Silver Strand Beach. Nice beach.

Any boat ride in the harbor would be cool. See all the new destroyers!

The old car and airplane museums in Balboa Park are fun.

You could drive down to the Mexico border and wave at the immigrants standing in line.

@josie I’ve never done the hop on/off bus ride in San Diego, but I’m a native San Diegan, so it’s not something that would have occured to me. But maybe next time I’m down there I’ll check it out. Well, not next time since I’m going to Comicon, but the time after that.

My sister just when on a seal watching boat tour.

In addition to everything that has been mentioned, I would recommend a dinner cruise of San Diego Bay.

Check out Hornblower Cruises:
https://www.hornblower.com/port/category/sd+diningcruises

The Birch Aquarium in La Jolla:
https://aquarium.ucsd.edu/

The Museum of Making Music in Carlsbad:
https://www.museumofmakingmusic.org/

See a show at the elegantly restored Balboa Theater:
https://theater-sandiego.com/balboa/?gclid=CjwKCAjw7_rlBRBaEiwAc23rhticoW1jSoVzKhOu8Sw3UFO-9skqElgIaNSkyruoCplyf1WmxbCPAhoC24gQAvD_BwE

Have lunch at Liberty Public Market at Liberty Station:
https://bluebridgehospitality.com/libertypublicmarket/

Go to one of the several Indian casinos to gamble, or eat at the buffet, or both, that are all within a half hour, to an hour and a half drive from Downtown San Diego including Pala, Pauma, Harrah’s Rincon, Valley View, Sycuan, or Viejas.

If you are going there in June or the beginning of July, go to the San Diego County Fair:
https://sdfair.com/

Have a casual breakfast or lunch alfresco at the Cliff Hanger Café, high above Blacks Beach and watch hang gliders and parasailers jump off the cliffs at The Torrey Pines Glider Port:
https://www.flytorrey.com/the-cafe/

Right behind the glider port is the campus of UCSD. If you like public art and interesting architecture, you can see the iconic UCSD Library building, and the University’s Stuart Collection:
http://stuartcollection.ucsd.edu/

Eat a fish taco (at pretty much any taco stand, or Mexican restaurant in San Diego), but if you want to eat one at the official birthplace of fish tacos in San Diego go to Rubio’s #1 at Mission Bay, and then enjoy yourself at the beach at Mission Bay:
https://www.rubios.com/restaurant-locations/california/san-diego/mission-bay

Visit the meditation garden at the Self Realization Fellowship Temple in Encinitas. It’s free to the public, and no one will try to indoctrinate you. It’s a plant lover’s haven that sits high above Swami’s beach, one of the best surfing spots in San Diego County:
http://www.encinitastemple.org/visiting/

Then have breakfast or lunch at Swami’s Cafe (across the street on highway 101):
http://swamiscafe.com/

If you like 50’s era diners, and the ocean, head to Ruby’s Diner on the pier at Oceanside:
https://www.rubys.com/locations/oceanside/

Get up to the Cuyamaca mountains, about an hour East of downtown San Diego, and visit the quaint, former gold mining town of Julian,and treat yourself to some famous apple pie, and see breathtaking views of the Anza Borrego Desert below, to the East:
https://www.sandiegofamily.com/travel/family-visit-to-julian

Stay at the Orchard Hill Country Inn Cottages:
https://www.orchardhill.com/

Ot The Julian Lodge:
http://www.julianlodge.com/

Have a great trip : )

Thank you, @Kardamom, for some awesome suggestions!