The Best Hotels in Mission Bay, San Diego - 2026 Updated Prices

An aerial view of a coastal city with a marina, a large body of water, and a peninsula with buildings.

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Hotels recommended for families in Mission Bay

A pool area with a hot tub, lounge chairs, and umbrellas.

The Dana on Mission Bay

Mission Bay

฿8,414 total

includes taxes & fees

9 Nov - 10 Nov

Where to stay in Mission Bay

Find the best Mission Bay areas for the activities you enjoy most.

A large stadium with the sign "Cobo Park" and palm trees around it.

Downtown San Diego

Known for its fantastic nightlife, fascinating museums and beautiful waterfront views, there's plenty to explore in Downtown San Diego. Top attractions like Petco Park and Port of San Diego are major draws. Catch the metro at Civic Center Station or Civic Center Station to see more of the city.

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A pier extending into the ocean with buildings at the end, under a partly cloudy sky.

Pacific Beach

Relax in beachside cafés in the morning, surf clean breaks in the afternoon and dance with a youthful club crowd at night at this coastal San Diego strip.

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Gaslamp Quarter

San Diego’s historic heart has shed its seedy past to emerge as one of the city’s premier dining, shopping and entertainment hubs.

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A coastal cityscape with a long sandy beach, a pier, and dense urban buildings.

Mission Beach

If you're spending some time in Mission Beach, Mission Bay and Mission Beach are top sights worth seeing.

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A coastal walkway with a statue, benches, and people.

Point Loma

Seaside views a bustling port and top sights from Marine Corps Recruit Depot to Shelter Island – discover Point Loma, a destination also famous for its island views.

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Top Mission Bay Hotel Reviews

Bay Club Hotel & Marina

10/10 Excellent

"We loved where the hotel was located! Lots of restaurants nearby. The rooms were a nice size. We had a view of the harbor. We would definitely stay here again!"

Frequently asked questions

What is Mission Bay like?

You'll be sure to have fun exploring San Diego's Mission Bay neighbourhood. Looking for sights you might find in a travel guide about Mission Bay? Consider a visit to Mission Bay while you're in the neighbourhood.

What's a favourite hotel to stay in Mission Bay?

Based on our traveller data, Paradise Point Resort & Spa is one of the top choices for your stay in Mission Bay. This resort is a short 1-minute walk from Mission Bay, and it offers a marina and 5 outdoor pools. Other good options for your stay in the neighbourhood include The Dana on Mission Bay and San Diego Mission Bay Resort.

How many hotels should I expect to find in the Mission Bay area?

If you're searching for places to stay in San Diego, Expedia has something to meet your needs with 37 Mission Bay hotels and other accommodation options to choose from.

If I need to cancel my hotel reservation in Mission Bay, will I receive a refund?

Yes, you'll find most room reservations are refundable provided that you cancel before the accommodation's cancellation deadline, which is usually within 24-48 hours of the scheduled arrival. If you booked a non-refundable reservation, you might be able to still cancel and be given a refund within a 24-hour period of your booking. Add your dates and click on "Search", then you can use the "fully refundable" filter to view top deals in Mission Bay.

What is there to do around this San Diego neighbourhood?

Enjoy a stroll along the shore at Ski Beach, Mission and Pacific Beaches and Crown Point Shores while you're in Mission Bay. You could also plan a visit to Mission Bay or North Cove Beach while you're in the neighbourhood. Don't miss favourite places to visit in the surrounding area, such as Mission Beach, Marine Corps Recruit Depot and Hotel Circle. When you're sightseeing in San Diego, The Dana On Mission Bay, BW Premier Collection and Marina Village Conference Center are also worth a stop.

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Our top choices for Mission Bay hotels

1. The Dana on Mission Bay

2. San Diego Mission Bay Resort

3. Paradise Point Resort & Spa

4. Hyatt Regency Mission Bay Spa and Marina

5. Holiday Inn Express San Diego - SeaWorld Area by IHG

6. Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town

7. Best Western Inn & Suites San Diego – Zoo/SeaWorld Area

8. Homewood Suites by Hilton San Diego Hotel Circle/SeaWorld Area

9. Hilton Garden Inn San Diego Old Town/SeaWorld Area

10. La Quinta Inn & Suites by Wyndham San Diego Mission Bay

11. Hampton Inn San Diego/Mission Valley

12. Crowne Plaza San Diego - Mission Valley by IHG

13. Wyndham Garden San Diego Near SeaWorld

14. GreenTree Inn San Diego Mission Bay

15. Holiday Inn Express San Diego Airport - Old Town by IHG

16. Bahia Resort Hotel

17. Best Western Plus Hacienda Hotel Old Town

18. Old Town Inn

19. Hampton Inn & Suites San Diego Airport Liberty Station

20. Homewood Suites by Hilton San Diego Airport/Liberty Station

Hotels recommended for families in Mission Bay

The Dana on Mission Bay

Where to stay in Mission Bay

Downtown San Diego

Pacific Beach

Gaslamp Quarter

Mission Beach

Point Loma

Top Mission Bay Hotel Reviews

Bay Club Hotel & Marina

Frequently asked questions