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

Our top choices for Mission Bay hotels

1. ITH Mission Beach Backpacker Hostel

Central Mission Beach, 2.4 km from Mission Bay

Julien

฿5,350 total

includes taxes & fees

25 Jun - 26 Jun

2. The Wayfarer San Diego

Mission Beach, 3 km from Mission Bay

Lily

฿11,794 total

includes taxes & fees

17 Jun - 18 Jun

2 outdoor pools, a heated pool, pool loungers

3. The Dana on Mission Bay

Mission Bay, 1.6 km from Mission Bay

Jamie

฿10,627 total

includes taxes & fees

18 Jun - 19 Jun

5 outdoor pools, a heated pool, pool umbrellas, pool loungers

4. Paradise Point Resort & Spa

Mission Bay, 1.3 km from Mission Bay

Myesha

฿12,170 total

includes taxes & fees

29 Jun - 30 Jun

Studio Suite, 1 King Bed, Courtyard View | View from room

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

3.2 km from Mission Bay

Gretchen

฿7,539 total

includes taxes & fees

18 Jun - 19 Jun

6. Bahia Resort Hotel

Central Mission Beach, 2 km from Mission Bay

Jon

฿13,554 total

includes taxes & fees

6 Jul - 7 Jul

Outdoor pool, open 7:00 AM to 10:00 PM, pool cabanas (surcharge)

7. San Diego Mission Bay Resort

Mission Bay, 1.5 km from Mission Bay

Lance

฿12,161 total

includes taxes & fees

7 Jul - 8 Jul

In-room safe, desk, laptop workspace, blackout curtains

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

2.5 km from Mission Bay

Angeline

฿7,864 total

includes taxes & fees

17 Jun - 18 Jun

9. Fairfield Inn & Suites by Marriott San Diego Pacific Beach

Pacific Beach, 2.9 km from Mission Bay

Jesus

฿6,396 total

includes taxes & fees

5 Jul - 6 Jul

3 outdoor pools, pool cabanas (surcharge), pool umbrellas

10. Hyatt Regency Mission Bay Spa and Marina

Mission Bay, 1.9 km from Mission Bay

Yesenia

฿11,414 total

includes taxes & fees

12 Jul - 13 Jul

11. Catamaran Resort and Spa

Mission Beach, 2.9 km from Mission Bay

Claudine

฿13,440 total

includes taxes & fees

29 Jun - 30 Jun

12. Best Western San Diego Pacific Beach/Mission Bay

2.5 km from Mission Bay

Aron

฿5,236 total

includes taxes & fees

29 Jun - 30 Jun

13. Surfer Beach Hotel

Pacific Beach, 3 km from Mission Bay

Aleta

฿9,295 total

includes taxes & fees

1 Jul - 2 Jul

14. GreenTree Inn San Diego Mission Bay

Pacific Beach, 3 km from Mission Bay

Tyson

฿6,028 total

includes taxes & fees

28 Jun - 29 Jun

Desk, laptop workspace, blackout curtains, iron/ironing board

15. SureStay Hotel by Best Western San Diego Pacific Beach

Pacific Beach, 3 km from Mission Bay

NORALYN

฿4,621 total

includes taxes & fees

17 Jun - 18 Jun

16. ITH Beach Bungalow Surf Hostel

Pacific Beach, 3.2 km from Mission Bay

mike

฿2,807 total

includes taxes & fees

7 Jul - 8 Jul

17. Heritage Inn San Diego

2.5 km from Mission Bay

Alyssa

฿2,711 total

includes taxes & fees

17 Jun - 18 Jun

18. Wyndham Garden San Diego Near SeaWorld

2.8 km from Mission Bay

Hector

฿4,941 total

includes taxes & fees

1 Jul - 2 Jul

19. Mission Bay Motel

Pacific Beach, 3 km from Mission Bay

Juan C

฿4,129 total

includes taxes & fees

5 Jul - 6 Jul

20. E-Z 8 Motel Old Town

Old Town San Diego, 3.1 km from Mission Bay

Ashley

฿3,149 total

includes taxes & fees

22 Jun - 23 Jun

View all properties

Compare popular hotels close to Mission Bay

Property	Property class	Guest rating
ITH Mission Beach Backpacker Hostel	2.0 star property	9.4 Exceptional 218 reviews	View
The Wayfarer San Diego	4.0 star property	9.4 Exceptional 1,799 reviews	View
The Dana on Mission Bay	3.5 star property	9.0 Wonderful 4,411 reviews	View
Paradise Point Resort & Spa	4.0 star property	8.8 Excellent 2,671 reviews	View
Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town	4.0 star property	9.2 Wonderful 1,047 reviews	View

Top Mission Bay Hotel Reviews

San Diego Mission Bay Resort

10/10 Excellent

"Staff were super friendly and helpful! So many things to do, I didn’t even get to enjoy them all! The dock activities was awesome. Ice machine broken on our floor, inconvient, but very small issue. No complaints! And centrally to lots of other places and beaches!! Would definitely stay again."

Comfort Inn Sea World Area

10/10 Excellent

"This hotel is so nicely renovated! The rooms still feel brand new. The parking is free and feels relatively secure even though it's not fully gated. The area is a little rough but I felt safe. It's so nice to have a hot breakfast included, and their outside patio is very cute. I had my dog with me; they put all dogs on the ground floor, and our room was on the back with a grass yard outside and it was nice and quiet. There is a Raising Cane's next door and a very cute coffee shop and plant nursery a few blocks away. The location was convenient to the beach and not far from UCSD. I wish the refrigerator had a freezer section but otherwise it was almost perfect! The staff and management were all very friendly and helpful too. Would definitely stay here again."

Hotels near other Mission Bay attractions

Ski Beach

Why not spend a lazy afternoon at Ski Beach during your trip to San Diego?

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Frequently asked questions

What's the area like around Mission Bay?

Mission Bay is located in a family-friendly area of San Diego known for its array of dining options and popular zoo. If you're looking for a convenient place to stay, take a look at the 46 hotels and other accommodation options you'll find within a mile.

What's the best place to stay near Mission Bay?

San Diego Mission Bay Resort is one of the top choices for your stay based on our traveller data, and this resort offers a full-service spa and 2 restaurants. It's located just a short 0.9 mi (1.5 km) from Mission Bay. Another good option is Paradise Point Resort & Spa, located just 0.8 mi (1.3 km) away.

How many hotels will I find near Mission Bay?

Expedia has 46 hotels and other accommodation options within a mile from Mission Bay.

If I need to cancel the hotel reservation for my stay near Mission Bay, will I receive a refund?

Yes! You'll find that most room reservations are fully refundable if cancelled prior to the hotel's cancellation deadline, which is usually within 24-48 hours of the scheduled arrival. If you booked a non-refundable reservation, you might still have the option to cancel and get a refund within 24 hours of booking. Enter your dates, click on "Search", then you can filter by "fully refundable" to view the best deals near Mission Bay.

What can I see and do near Mission Bay?

Study the collections at Whaley House Museum, Maritime Museum of San Diego or Junipero Serra Museum. Mason Street School, Casa de Machado y Stewart and McCoy Museum House are well-known local landmarks worth a visit. You can catch a show at Humphreys Concerts by the Bay, San Diego Black Ensemble Theater and Cygnet Theater Company.

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Our top choices for Mission Bay hotels

1. ITH Mission Beach Backpacker Hostel

2. The Wayfarer San Diego

3. The Dana on Mission Bay

4. Paradise Point Resort & Spa

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

6. Bahia Resort Hotel

7. San Diego Mission Bay Resort

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

9. Fairfield Inn & Suites by Marriott San Diego Pacific Beach

10. Hyatt Regency Mission Bay Spa and Marina

11. Catamaran Resort and Spa

12. Best Western San Diego Pacific Beach/Mission Bay

13. Surfer Beach Hotel

14. GreenTree Inn San Diego Mission Bay

15. SureStay Hotel by Best Western San Diego Pacific Beach

16. ITH Beach Bungalow Surf Hostel

17. Heritage Inn San Diego

18. Wyndham Garden San Diego Near SeaWorld

19. Mission Bay Motel

20. E-Z 8 Motel Old Town

Compare popular hotels close to Mission Bay

Top Mission Bay Hotel Reviews

San Diego Mission Bay Resort

Hotels near other Mission Bay attractions

Ski Beach

Frequently asked questions