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

Jessi

฿4,544 total

includes taxes & fees

8 Jun - 9 Jun

2. Boardwalk Hotel: Bikes, Boards & Beach Gear Included

Mission Beach, 2.4 km from Mission Bay

Amanda

฿9,851 total

includes taxes & fees

8 Jun - 9 Jun

2 outdoor pools, a heated pool, pool loungers

3. The Dana on Mission Bay

Mission Bay, 1.6 km from Mission Bay

René

฿9,952 total

includes taxes & fees

15 Jun - 16 Jun

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

4. Paradise Point Resort & Spa

Mission Bay, 1.3 km from Mission Bay

Daniel

฿11,658 total

includes taxes & fees

14 Jun - 15 Jun

5. The Wayfarer San Diego

Mission Beach, 3 km from Mission Bay

Lily

฿11,882 total

includes taxes & fees

9 Jun - 10 Jun

6. Bahia Resort Hotel

Central Mission Beach, 2 km from Mission Bay

Oswaldo

฿8,921 total

includes taxes & fees

10 Jun - 11 Jun

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

Jean-Michelle

฿12,629 total

includes taxes & fees

14 Jun - 15 Jun

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

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

2.5 km from Mission Bay

Isela

฿6,748 total

includes taxes & fees

14 Jun - 15 Jun

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

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

3.2 km from Mission Bay

Angela

฿5,994 total

includes taxes & fees

8 Jun - 9 Jun

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

฿10,217 total

includes taxes & fees

17 Jun - 18 Jun

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

Pacific Beach, 2.9 km from Mission Bay

Jesus

฿5,768 total

includes taxes & fees

15 Jun - 16 Jun

12. Best Western San Diego Pacific Beach/Mission Bay

2.5 km from Mission Bay

Richard

฿4,486 total

includes taxes & fees

17 Jun - 18 Jun

13. Catamaran Resort and Spa

Mission Beach, 2.9 km from Mission Bay

Alexandre

฿11,454 total

includes taxes & fees

17 Jun - 18 Jun

14. Comfort Inn Sea World Area

3.2 km from Mission Bay

Fernando

฿4,712 total

includes taxes & fees

8 Jun - 9 Jun

15. GreenTree Inn San Diego Mission Bay

Pacific Beach, 3 km from Mission Bay

Victoria

฿5,055 total

includes taxes & fees

8 Jun - 9 Jun

16. Surfer Beach Hotel

Pacific Beach, 3 km from Mission Bay

Sondra

฿8,427 total

includes taxes & fees

16 Jun - 17 Jun

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

17. SureStay Hotel by Best Western San Diego Pacific Beach

Pacific Beach, 3 km from Mission Bay

Michael

฿4,075 total

includes taxes & fees

8 Jun - 9 Jun

18. ITH Beach Bungalow Surf Hostel

Pacific Beach, 3.2 km from Mission Bay

mike

฿2,466 total

includes taxes & fees

14 Jun - 15 Jun

19. Heritage Inn San Diego

2.5 km from Mission Bay

Latrice

฿2,731 total

includes taxes & fees

14 Jun - 15 Jun

20. Wyndham Garden San Diego Near SeaWorld

2.8 km from Mission Bay

Aaron

฿4,262 total

includes taxes & fees

15 Jun - 16 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 216 reviews	View
Boardwalk Hotel: Bikes, Boards & Beach Gear Included	3.0 star property	9.4 Exceptional 381 reviews	View
The Dana on Mission Bay	3.5 star property	9.0 Wonderful 4,385 reviews	View
Paradise Point Resort & Spa	4.0 star property	8.8 Excellent 2,637 reviews	View
The Wayfarer San Diego	4.0 star property	9.4 Exceptional 1,791 reviews	View

Top Mission Bay Hotel Reviews

Paradise Point Resort & Spa

10/10 Excellent

"Our family had a great time! We enjoyed the pools, kayaking, and having dinner outside next to the water. We will definitely be back :)"

Best Western San Diego Pacific Beach/Mission Bay

8/10 Good

"Good location very clean and nice breakfast. My only problem was I could hear the next door rooms doors close and hear people above me and to the adjoining rooms walking around until almost 2 am. If you are a light sleeper this might not be the place. But otherwise 5 stars"

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

10/10 Excellent

"Great experience. Rooms were clean and the hotel felt very clean and updated. Only stayed for a night before heading north, so I can’t speak to the location, but overall we had a great one night stay. Would recommend."

The Alcala Hotel Mission Valley/Seaworld

6/10 Okay

"I feel like if I'm staying at a hotel the least they can do is have bars of soap and toiletries. The complimentary breakfast was not complimentary at all the only good thing about the breakfast they have to offer is the waffles and that's because you make them yourself and the Yoplait yogurt was good. The rooms are outdated and I recommend going across the street to the Best Western it would have been better."

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?

Paradise Point Resort & Spa is one of the top choices for your stay based on our traveller data, and this resort offers a marina and 5 outdoor pools. It's located just a short 0.8 mi (1.3 km) from Mission Bay. Another good option is San Diego Mission Bay Resort, located just 0.9 mi (1.5 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 Maritime Museum of San Diego, Whaley House Museum or Junipero Serra Museum. Casa de Machado y Stewart, McCoy Museum House and Casa de Estudillo 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. Boardwalk Hotel: Bikes, Boards & Beach Gear Included

3. The Dana on Mission Bay

4. Paradise Point Resort & Spa

5. The Wayfarer San Diego

6. Bahia Resort Hotel

7. San Diego Mission Bay Resort

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

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

10. Hyatt Regency Mission Bay Spa and Marina

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

12. Best Western San Diego Pacific Beach/Mission Bay

13. Catamaran Resort and Spa

14. Comfort Inn Sea World Area

15. GreenTree Inn San Diego Mission Bay

16. Surfer Beach Hotel

17. SureStay Hotel by Best Western San Diego Pacific Beach

18. ITH Beach Bungalow Surf Hostel

19. Heritage Inn San Diego

20. Wyndham Garden San Diego Near SeaWorld

Compare popular hotels close to Mission Bay

Top Mission Bay Hotel Reviews

Paradise Point Resort & Spa

Hotels near other Mission Bay attractions

Ski Beach

Frequently asked questions