The Best Hotels Closest to Mission Bay in San Diego for 2026

Our top choices for Mission Bay hotels

2 outdoor pools, a heated pool, sun loungers

The Dana on Mission Bay

Mission Bay, 1.6 km from Mission Bay

Jamie

₩451,693 total

includes taxes & fees

Jun 17 - Jun 18

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

Paradise Point Resort & Spa

Mission Bay, 1.3 km from Mission Bay

Myesha

₩547,676 total

includes taxes & fees

Jun 18 - Jun 19

The Wayfarer San Diego

Mission Beach, 3 km from Mission Bay

Lily

₩459,004 total

includes taxes & fees

Jun 16 - Jun 17

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

San Diego Mission Bay Resort

Mission Bay, 1.5 km from Mission Bay

Lance

₩566,788 total

includes taxes & fees

Jun 29 - Jun 30

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

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

3.2 km from Mission Bay

Angela

₩312,168 total

includes taxes & fees

Jun 16 - Jun 17

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

Holiday Inn Express San Diego - SeaWorld Area by IHG

2.5 km from Mission Bay

Angeline

₩347,050 total

includes taxes & fees

Jun 17 - Jun 18

3 outdoor pools, cabanas (surcharge), pool umbrellas

Hyatt Regency Mission Bay Spa and Marina

Mission Bay, 1.9 km from Mission Bay

Yesenia

₩399,423 total

includes taxes & fees

Jun 17 - Jun 18

Comfort Inn Sea World Area

3.2 km from Mission Bay

Fernando

₩226,719 total

includes taxes & fees

Jun 16 - Jun 17

Catamaran Resort and Spa

Mission Beach, 2.9 km from Mission Bay

Claudine

₩494,355 total

includes taxes & fees

Jun 18 - Jun 19

Best Western San Diego Pacific Beach/Mission Bay

2.5 km from Mission Bay

Richard

₩244,015 total

includes taxes & fees

Jun 28 - Jun 29

GreenTree Inn San Diego Mission Bay

Pacific Beach, 3 km from Mission Bay

Tyson

₩249,567 total

includes taxes & fees

Jun 16 - Jun 17

Surfer Beach Hotel

Pacific Beach, 3 km from Mission Bay

Aleta

₩430,845 total

includes taxes & fees

Jul 1 - Jul 2

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

SureStay Hotel by Best Western San Diego Pacific Beach

Pacific Beach, 3 km from Mission Bay

NORALYN

₩217,631 total

includes taxes & fees

Jun 16 - Jun 17

ITH Beach Bungalow Surf Hostel

Pacific Beach, 3.2 km from Mission Bay

mike

₩114,079 total

includes taxes & fees

Jun 16 - Jun 17

Heritage Inn San Diego

2.5 km from Mission Bay

Alyssa

₩119,809 total

includes taxes & fees

Jun 28 - Jun 29

Wyndham Garden San Diego Near SeaWorld

2.8 km from Mission Bay

Hector

₩207,533 total

includes taxes & fees

Jun 16 - Jun 17

E-Z 8 Motel Old Town

Old Town San Diego, 3.1 km from Mission Bay

Ashley

₩146,745 total

includes taxes & fees

Jun 16 - Jun 17

Mission Bay Motel

Pacific Beach, 3 km from Mission Bay

Juan C

₩200,149 total

includes taxes & fees

Jun 16 - Jun 17

Pacific Terrace Hotel

North Pacific Beach, 3.8 km from Mission Bay

Phillip

₩602,750 total

includes taxes & fees

Jun 17 - Jun 18

Tower23 Hotel

North Pacific Beach, 3.5 km from Mission Bay

michael

₩615,191 total

includes taxes & fees

Jun 17 - Jun 18

View all properties

Compare popular hotels close to Mission Bay

Property	Property class	Guest rating
The Dana on Mission Bay	3.5 star property	9.0 Wonderful 4,405 reviews	View
Paradise Point Resort & Spa	4.0 star property	8.8 Excellent 2,670 reviews	View
The Wayfarer San Diego	4.0 star property	9.4 Exceptional 1,799 reviews	View
San Diego Mission Bay Resort	4.0 star property	8.6 Excellent 1,489 reviews	View
Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town	4.0 star property	9.2 Wonderful 1,044 reviews	View

Top Mission Bay Hotel Reviews

GreenTree Inn San Diego Mission Bay

6/10 Okay

"Rooms need more upkeep! Bathtub was dirty and blankets had stains."

The Dana on Mission Bay

10/10 Excellent

"I love the lush greenery! A great getaway from the hustle of the beaches which is where we spent most of our time. My kids loved movie night at the pool. The rooms are big and very clean, the beds are comfy. Only drawback that I wasn’t expecting was $35/night for parking. I would definitely stay here again."

Wyndham Garden San Diego Near SeaWorld

4/10 Poor

"I was honestly shocked that there were roaches in our room. We only stayed for one night. Also the ice machine near our room was out of order. The pool was nice and the staff was helpful when their affiliate did not send my booking in time. It took a few hours so we had to wait in the lobby until rectified."

Comfort Inn Sea World Area

2/10 Terrible

"If I could give zero stars I would. Had a horrible experience and they have very bad customer service. Don't stay here! avoid at all costs. We booked a room overnight and when using the shower we discovered it was clogged. The tub would fill and you had to be in dirty tub water in order to shower and the water would not leave until 30 minutes after you were done showering. We called the front desk for someone to come fix it and they sent someone who checked it out and said that they would need to put chemicals and the only thing they could do since we were only staying overnight was to put a note stating we weren't responsible for the shower being clogged. We paid for our room, it's not like we got it for free. When you book a room you do so with the assumption that everything in it works, specially the shower. We were in disbelief that they're only solution was to not blame us for it. They didn't offer another room with a working shower or to fix the shower in the room they gave us. No one was able to shower after we discovered it was clogged. The next morning when checking out I spoke to a manager about it. And her solution was no refunds, and that she could give me a discount on our next stay, I told her we're never staying here again, and again asked for a partial refund. She stated they don't do refunds and that we could get some snacks from their snack bar. So beware! Don't come here unless you want chips as compensation for your horrible stay."

Hotels near other Mission Bay attractions

Ski Beach

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

See properties

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, check out the 46 hotels and other accommodations you'll find within a mile.

Where is 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 traveler 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 can I expect to find close to Mission Bay?

Expedia has 46 hotels and other accommodations 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 hotel bookings are fully refundable provided that you cancel before the hotel's cancellation deadline, which in most cases is within 24 or 48 hours of your arrival date. If your reservation is non-refundable, you may still be able to cancel and be given a refund within 24 hours of booking. Enter your dates, click on "Search", then filter by "fully refundable" to review the top deals on offer near Mission Bay.

Where can I learn more about changing or cancelling my trip in the area near Mission Bay?

For more details about picking new dates or cancelling your stay near Mission Bay, head over to our customer service page.

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

The Dana on Mission Bay

Paradise Point Resort & Spa

The Wayfarer San Diego

San Diego Mission Bay Resort

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

Holiday Inn Express San Diego - SeaWorld Area by IHG

Hyatt Regency Mission Bay Spa and Marina

Comfort Inn Sea World Area

Catamaran Resort and Spa

Best Western San Diego Pacific Beach/Mission Bay

GreenTree Inn San Diego Mission Bay

Surfer Beach Hotel

SureStay Hotel by Best Western San Diego Pacific Beach

ITH Beach Bungalow Surf Hostel

Heritage Inn San Diego

Wyndham Garden San Diego Near SeaWorld

E-Z 8 Motel Old Town

Mission Bay Motel

Pacific Terrace Hotel

Tower23 Hotel

Compare popular hotels close to Mission Bay

Top Mission Bay Hotel Reviews

GreenTree Inn San Diego Mission Bay

Hotels near other Mission Bay attractions

Ski Beach

Frequently asked questions

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