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Our top choices for Mission Bay hotels

The Dana on Mission Bay

The Dana on Mission Bay
3.5 star property
Mission Bay, 1.6 km from Mission Bay
9.0 out of 10, Wonderful, (4,287 reviews)
"Beautiful bay view and very quiet. Loved that the restaurant on the marina was steps from my building. "
United States
Sara
The price is ฿5,729
฿7,321 total
includes taxes & fees
10 May - 11 May
The Dana on Mission Bay

Boardwalk Hotel: Bikes, Boards & Beach Gear Included

Boardwalk Hotel: Bikes, Boards & Beach Gear Included
3.0 star property
Mission Beach, 2.4 km from Mission Bay
9.4 out of 10, Exceptional, (340 reviews)
"Great access to the ocean and Mission Bay. "
United States
Lisa
The price is ฿5,004
฿5,642 total
includes taxes & fees
11 May - 12 May
Boardwalk Hotel: Bikes, Boards & Beach Gear Included

ITH Mission Beach Backpacker Hostel

ITH Mission Beach Backpacker Hostel
2.0 star property
Central Mission Beach, 2.4 km from Mission Bay
9.4 out of 10, Exceptional, (207 reviews)
"I’ve stayed at ITH Mission Beach a few times and every time I enjoy my stay. They offer many activities to do, the staff is very friendly and you can’t beat the location. One of the better hostels in San Diego. I highly recommend . "
United States
Kimberley
The price is ฿4,000
฿4,510 total
includes taxes & fees
28 Apr - 29 Apr
ITH Mission Beach Backpacker Hostel

Paradise Point Resort & Spa

Paradise Point Resort & Spa
4.0 star property
Mission Bay, 1.3 km from Mission Bay
8.8 out of 10, Excellent, (2,543 reviews)
"Everything was really nice and clean. Staff was very attentive and helpful and a great place right on the water in mission bay. "
United States
Stephen
The price is ฿6,659
฿9,348 total
includes taxes & fees
26 Apr - 27 Apr
Paradise Point Resort & Spa

The Wayfarer San Diego

The Wayfarer San Diego
4.0 star property
Mission Beach, 3 km from Mission Bay
9.4 out of 10, Exceptional, (1,765 reviews)
"Great location. Older refurbished hotel on Pacific Beach."
United States
Rachel
The price is ฿8,659
฿9,954 total
includes taxes & fees
29 Apr - 30 Apr
The Wayfarer San Diego

Holiday Inn Express San Diego - SeaWorld Area by IHG

Holiday Inn Express San Diego - SeaWorld Area by IHG
2.5 star property
2.5 km from Mission Bay
9.0 out of 10, Wonderful, (1,005 reviews)
"Great location and friendly staff. Just as described. Very happy with our stay."
United States
Bruna
The price is ฿4,481
฿5,151 total
includes taxes & fees
26 Apr - 27 Apr
Holiday Inn Express San Diego - SeaWorld Area by IHG

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

Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town
3.0 star property
3.2 km from Mission Bay
9.2 out of 10, Wonderful, (857 reviews)
"great room great breakfast and comfortable beds"
United States
Fany
The price is ฿4,744
฿5,453 total
includes taxes & fees
26 Apr - 27 Apr
Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town

San Diego Mission Bay Resort

San Diego Mission Bay Resort
4.0 star property
Mission Bay, 1.5 km from Mission Bay
8.4 out of 10, Very good, (1,423 reviews)
"We had a great stay and very pleasant vacation at Mission Bay Resort. Confortable and nice."
United States
Marta
The price is ฿7,010
฿9,750 total
includes taxes & fees
26 Apr - 27 Apr
San Diego Mission Bay Resort

Bahia Resort Hotel

Bahia Resort Hotel
3.5 star property
Central Mission Beach, 2 km from Mission Bay
8.6 out of 10, Excellent, (2,002 reviews)
"Good resort. The beach and gardens were calm and clean. Wish we had a few more days to just relax on the Bay front."
United States
Darren
The price is ฿5,719
฿8,348 total
includes taxes & fees
30 Apr - 1 May
Bahia Resort Hotel

The Beach Cottages

The Beach Cottages
2.5 star property
Pacific Beach, 3.2 km from Mission Bay
9.2 out of 10, Wonderful, (1,000 reviews)
"lovely beach vibe. perfect little getaway spot. close to plenty of restaurants and bars and cute little shops. This will be our first pick if we visit the area again"
United States
John Adam W
The price is ฿5,580
฿6,414 total
includes taxes & fees
28 Apr - 29 Apr
The Beach Cottages

Hyatt Regency Mission Bay Spa and Marina

Hyatt Regency Mission Bay Spa and Marina
4.0 star property
Mission Bay, 1.9 km from Mission Bay
8.4 out of 10, Very good, (1,617 reviews)
"Wonderful place to stay, especially with kiddos. The breakfast package is a must and an ocean view room really puts the whole vibe above and w"
United States
James
The price is ฿5,409
฿7,911 total
includes taxes & fees
10 May - 11 May
Hyatt Regency Mission Bay Spa and Marina

Fairfield Inn & Suites by Marriott San Diego Pacific Beach

Fairfield Inn & Suites by Marriott San Diego Pacific Beach
3.0 star property
Pacific Beach, 2.9 km from Mission Bay
8.8 out of 10, Excellent, (877 reviews)
"Great property right off the freeway. Close to playground and mission bay. A few minute drive to plenty of food option in pacific beach Traffic can be noisy since it’s right off the freeway"
United States
Christopher
The price is ฿4,193
฿4,820 total
includes taxes & fees
10 May - 11 May
Fairfield Inn & Suites by Marriott San Diego Pacific Beach

Best Western San Diego Pacific Beach/Mission Bay

Best Western San Diego Pacific Beach/Mission Bay
2.5 star property
Bay Park, 2.5 km from Mission Bay
8.2 out of 10, Very good, (359 reviews)
"Everything is freshly renewed, smells great , breakfast included & close to alot of things! Mission Bay is across the bridge with lots of play area for the littles! Loved it "
United States
Blanca
The price is ฿3,344
฿3,843 total
includes taxes & fees
4 May - 5 May
Best Western San Diego Pacific Beach/Mission Bay

Comfort Inn Sea World Area

Comfort Inn Sea World Area
3.5 star property
3.2 km from Mission Bay
8.6 out of 10, Excellent, (3,595 reviews)
"Clean & comfortable room, nice breakfast, great location"
United States
Leydi C
The price is ฿3,313
฿3,808 total
includes taxes & fees
10 May - 11 May
Comfort Inn Sea World Area

GreenTree Inn San Diego Mission Bay

GreenTree Inn San Diego Mission Bay
2.5 star property
Pacific Beach, 3 km from Mission Bay
8.0 out of 10, Very good, (2,037 reviews)
"If you need a place to lay your head and have breakfast in the morn, this works. Small rooms. First floor smells like a marijuana farm. Only benefit is that it’s central to La Jolla- Old Town- Pacific Beach areas. Probably won’t stay here again unless I have to. "
United States
Christine
The price is ฿3,344
฿3,844 total
includes taxes & fees
27 Apr - 28 Apr
GreenTree Inn San Diego Mission Bay

Surfer Beach Hotel

Surfer Beach Hotel
3.0 star property
Pacific Beach, 3 km from Mission Bay
8.2 out of 10, Very good, (1,260 reviews)
"Staff was super friendly. They upgraded us to an oceanfront room for free since they had availabilities, I didn't even ask for it! Location is perfect, right on the beach in the middle of all the action. Fell asleep listening to the waves"
United States
Melanie
The price is ฿6,881
฿7,772 total
includes taxes & fees
13 May - 14 May
Surfer Beach Hotel

SureStay Hotel by Best Western San Diego Pacific Beach

SureStay Hotel by Best Western San Diego Pacific Beach
2.5 star property
Pacific Beach, 3 km from Mission Bay
8.0 out of 10, Very good, (1,565 reviews)
"Rooms are small but clean and comfy, breakfast was good, personnel was friendly. Location is close to all SD activities."
United States
Polina
The price is ฿3,337
฿3,769 total
includes taxes & fees
28 Apr - 29 Apr
SureStay Hotel by Best Western San Diego Pacific Beach

ITH Beach Bungalow Surf Hostel

ITH Beach Bungalow Surf Hostel
2.0 star property
Pacific Beach, 3.2 km from Mission Bay
8.0 out of 10, Very good, (257 reviews)
"What an amazing bunch of people running the most comfortable place in all of San Diego. "
United States
Jerry
The price is ฿4,459
฿5,028 total
includes taxes & fees
28 Apr - 29 Apr
ITH Beach Bungalow Surf Hostel

Heritage Inn San Diego

Heritage Inn San Diego
2.0 star property
2.5 km from Mission Bay
7.4 out of 10, Good, (1,394 reviews)
"We had a great stay 10/10/25-10/12/25…The hotel is in a great location to get to Mission Beach, Sea World, and the Downtown Harbor Blvd locations…The hotel was very clean, the hot tub was so relaxing, and the staff were so friendly.."
United States
Regina
The price is ฿2,175
฿2,499 total
includes taxes & fees
22 Apr - 23 Apr
Heritage Inn San Diego

Wyndham Garden San Diego Near SeaWorld

Wyndham Garden San Diego Near SeaWorld
3.0 star property
2.8 km from Mission Bay
7.4 out of 10, Good, (4,210 reviews)
"We stayed one night due to a delayed flight. The place was clean & tidy, the pool was fantastic. Staff was amazing. Great for a short budget friendly stay. "
United States
Karla
The price is ฿3,809
฿4,378 total
includes taxes & fees
26 Apr - 27 Apr
Wyndham Garden San Diego Near SeaWorld
Lowest nightly price found within the past 24 hours based on a 1 night stay for 2 adults. Prices and availability subject to change. Additional terms may apply.

Compare popular hotels close to Mission Bay

Property
Property class
Guest rating
Breakfast included
Pool
Spa
Pet-friendly
WiFi included
2 outdoor pools, a heated pool, pool loungers
The Dana on Mission Bay
3.5 star property
9.0
Wonderful
4,287 reviews
View
Exterior
Boardwalk Hotel: Bikes, Boards & Beach Gear Included
3.0 star property
9.4
Exceptional
340 reviews
View
Living area
ITH Mission Beach Backpacker Hostel
2.0 star property
9.4
Exceptional
207 reviews
View
5 outdoor pools, a heated pool, pool umbrellas, pool loungers
Paradise Point Resort & Spa
4.0 star property
8.8
Excellent
2,543 reviews
View
View from property
The Wayfarer San Diego
4.0 star property
9.4
Exceptional
1,765 reviews
View

Top Mission Bay Hotel Reviews

Hotels near other Mission Bay attractions

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 48 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 48 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, Cygnet Theater Company and Red Spade Theater.