Tour the Aircraft Carrier USS Midway, nearby Seaport Village is also nice. Coronado Island has the historic Hotel Del Coronado built in 1886. North of San Diego in La Jolla has a pretty cool cove with seals.
It's world famous, beautiful, and dirt cheap if I recall correctly. My fiance and I spent 8 hours there one day and we still didn't see everything because its so massive.
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We didn't have the chance to do much when we were there in April, but I'll echo the suggestions for the USS Midway, the San Diego Zoo and Seaport Village. There's a little restaurant right overtop the water in Seaport Village that is pretty good.
People have already mentioned the obvious
- Zoo/Balboa Park
- Sea World
- Sea Port village
- Safari Park (A little bit of a drive from downtown San Diego)
- Coronado
- La Jolla Shores Beach. Great beach to take your family to.
- Children's pool in La Jolla. Large seal population has made the beach their home.
- Birch Aquarium. It is a small aquarium near UCSD.
- Cabrillo National Monument in Point Loma. If it is clear there are great views of down town San Diego and Coronado (including the Naval base)
- Harbour cruise. There are several that you can take and have a tour of the harbour.
For food:
- Rubio's is a popular fast food 'mexican' restaurant. Fish tacos are a popular menu item. Roberto's is okay.
- IN-N-Out. Check out the 'secret' menu online.
- Mama Testa Taqueira. This is a great mexican restaurant.
Where are you planning on staying?
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If you want a great burger, try Hodad's. Avoid prime meal times as the line can go outside and around the corner. Yes, it's that good. The kids will love the car that's turned into an eating area.
My kids liked legoland
They loved Sea World, but man is it expensive. If they are young though, there is a sesame street area that made the hole trip worth it.
Zoo was good.
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San Diego is such an awesome city. A must is the USS Midway for sure. Padre games are fantastic. Just walking around down by the ocean is great.
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Thankfully you are going next week and will miss the Comic-Con crowds. There were quite a few grumpy people in the lobby today complaining about traffic/not being able to leave the parking lots.
Great suggestions already - it was nice to just walk around Seaport Village. We also enjoyed the food at the nearby Harbor House.