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

฿5,227 total

includes taxes & fees

14 Jun - 15 Jun

2 outdoor pools, a heated pool, pool loungers

2. The Dana on Mission Bay

Mission Bay, 1.6 km from Mission Bay

Jamie

฿9,631 total

includes taxes & fees

16 Jun - 17 Jun

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

3. Paradise Point Resort & Spa

Mission Bay, 1.3 km from Mission Bay

Myesha

฿11,703 total

includes taxes & fees

14 Jun - 15 Jun

4. The Wayfarer San Diego

Mission Beach, 3 km from Mission Bay

Lily

฿10,845 total

includes taxes & fees

14 Jun - 15 Jun

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

Mission Beach, 2.4 km from Mission Bay

Amanda

฿10,713 total

includes taxes & fees

16 Jun - 17 Jun

6. Bahia Resort Hotel

Central Mission Beach, 2 km from Mission Bay

Oswaldo

฿9,728 total

includes taxes & fees

15 Jun - 16 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

฿11,921 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

Angeline

฿7,137 total

includes taxes & fees

14 Jun - 15 Jun

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

Pacific Beach, 2.9 km from Mission Bay

Jesus

฿6,457 total

includes taxes & fees

17 Jun - 18 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

฿9,026 total

includes taxes & fees

14 Jun - 15 Jun

11. Catamaran Resort and Spa

Mission Beach, 2.9 km from Mission Bay

Alexandre

฿11,499 total

includes taxes & fees

17 Jun - 18 Jun

12. Comfort Inn Sea World Area

3.2 km from Mission Bay

Fernando

฿4,598 total

includes taxes & fees

16 Jun - 17 Jun

13. Best Western San Diego Pacific Beach/Mission Bay

2.5 km from Mission Bay

Richard

฿3,963 total

includes taxes & fees

17 Jun - 18 Jun

14. GreenTree Inn San Diego Mission Bay

Pacific Beach, 3 km from Mission Bay

Tyson

฿4,874 total

includes taxes & fees

15 Jun - 16 Jun

15. Surfer Beach Hotel

Pacific Beach, 3 km from Mission Bay

Aleta

฿9,944 total

includes taxes & fees

14 Jun - 15 Jun

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

16. SureStay Hotel by Best Western San Diego Pacific Beach

Pacific Beach, 3 km from Mission Bay

Michael

฿4,254 total

includes taxes & fees

16 Jun - 17 Jun

17. ITH Beach Bungalow Surf Hostel

Pacific Beach, 3.2 km from Mission Bay

mike

฿2,470 total

includes taxes & fees

14 Jun - 15 Jun

18. Heritage Inn San Diego

2.5 km from Mission Bay

Alyssa

฿2,735 total

includes taxes & fees

14 Jun - 15 Jun

19. Wyndham Garden San Diego Near SeaWorld

2.8 km from Mission Bay

Hector

฿4,278 total

includes taxes & fees

16 Jun - 17 Jun

20. Mission Bay Motel

Pacific Beach, 3 km from Mission Bay

Juan C

฿3,167 total

includes taxes & fees

18 Jun - 19 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 217 reviews	View
The Dana on Mission Bay	3.5 star property	9.0 Wonderful 4,399 reviews	View
Paradise Point Resort & Spa	4.0 star property	8.8 Excellent 2,653 reviews	View
The Wayfarer San Diego	4.0 star property	9.4 Exceptional 1,791 reviews	View
Boardwalk Hotel: Bikes, Boards & Beach Gear Included	3.0 star property	9.2 Wonderful 384 reviews	View

Top Mission Bay Hotel Reviews

Heritage Inn San Diego

2/10 Terrible

"Was worst stay ever… booked 2 nights stayed 1. Beds were terrible noisy traffic loud motorcycle and very thin windows! Get very sketchy."

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

8/10 Good

"Overall, our stay was good; however, we had a couple of issues took away from the perfect stay. Checked in: flawless. Front desk staff: great. (Although I missed parking was $25 when I booked. A little steep!) We stepped into a beautifully clean room. After getting changed, we left for a while, when we returned, WHAT A MESS the parking lot was! Cars were everywhere; no parking spots & cars were double parked in the road. 15 mins later, I finally was able to talk to the valet, who informed me we would have to get turned around and park behind a row of cars for now, and he would double park it later. After a multi-point turn around, I finally made it. 25 mins after arriving at the hotel, we finally were able to get to our room. I had my 7-year-old granddaughter with me, who was so tired, I would have liked to use that 25 mins getting her in bed! We slept well, in a most comfortable bed. When we went down to breakfast...to a line that took over 25 mins to get to the food; which was very sparce by then. The kitchen staff brought out 1 pan of eggs, no meat, & informed the rest of us, which were still quite a few, that breakfast closed at 10, and no more food was coming out except for 6 cups of batter for waffles. I chose to not get food for me and let the mothers with children behind me to have what was remaining. The way that the staff spoke was so disappointing. It was obvious that the kitchen/dining area, much like the parking lot, are too small for the number of rooms."

Best Western San Diego Pacific Beach/Mission Bay

2/10 Terrible

"Avoid this property. I booked this property based on the reviews I had read on Expedia. We'll those positive reviews are misleading. This property is awful. 1st off the staff is unresponsive and needs to be retrained in customer service. Our hair dryer didn't work. When my wife went to ask for a new one she was told no. Another person staying in another room gave us theirs. Secondly, the room smelled like cigarette smoke. For a non-smoking room it smelled like someone regularly smokes in there. Third there were ants in the sink and on the counter. And 4th and most disgusting on our last morning a roach the size of a silver dollar was in our bathroom. The breakfast that they advertise as having waffles and eggs didn't. Just hard boiled eggs in a plastic container already peeled collecting germs. All in all a horrible experience. We will never frequent tjis location again. And I encourage Expedia to remove this location from there offerings."

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 Maritime Museum of San Diego, Whaley House Museum 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 Dana on Mission Bay

3. Paradise Point Resort & Spa

4. The Wayfarer San Diego

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

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. Comfort Inn Sea World Area

13. Best Western San Diego Pacific Beach/Mission Bay

14. GreenTree Inn San Diego Mission Bay

15. Surfer Beach Hotel

16. SureStay Hotel by Best Western San Diego Pacific Beach

17. ITH Beach Bungalow Surf Hostel

18. Heritage Inn San Diego

19. Wyndham Garden San Diego Near SeaWorld

20. Mission Bay Motel

Compare popular hotels close to Mission Bay

Top Mission Bay Hotel Reviews

Heritage Inn San Diego

Hotels near other Mission Bay attractions

Ski Beach

Frequently asked questions