Search Hotels Near Mission Bay, San Diego

Start date: Check-in selected.
To Date
End date: Check-out

  • Change your mind

    Book hotels with free cancellation

  • Treat yourself

    Sign in to save 10% or more on thousands of hotels
    Sign in

  • Be picky

    Search almost a million properties worldwide

Check prices for these dates

Tonight
21 Dec - 22 Dec
Tomorrow
22 Dec - 23 Dec
Next weekend
26 Dec - 28 Dec
In two weeks
2 Jan - 4 Jan

Filter by

Guest rating
Guest rating
Star rating

Our top choices for Mission Bay hotels

Living area
ITH Mission Beach Backpacker Hostel

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, (201)
"great location and free parking available across the street. "
United States
Saquib
ITH Mission Beach Backpacker Hostel
Luxury Suite, 2 Bedrooms, Patio, Ocean View | Individually decorated, individually furnished, free WiFi, bed sheets
Boardwalk Hotel: Bikes, Boards & Beach Gear Included

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, (267)
"The hotel is in a great location, between the bay and ocean. We especially enjoyed the access to the bikes and beach chairs! "
United States
Laura
The price is ฿4,779
฿5,388 total
includes taxes & fees
12 Jan - 13 Jan 2026
Boardwalk Hotel: Bikes, Boards & Beach Gear Included
Outdoor pool, a heated pool
The Wayfarer San Diego

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, (1716)
"Great location great staff great stay. Would stay again "
United States
Regina
The price is ฿5,630
฿6,471 total
includes taxes & fees
22 Dec - 23 Dec
The Wayfarer San Diego
Reception
Hampton Inn & Suites by Hilton San Diego SeaWorld

Hampton Inn & Suites by Hilton San Diego SeaWorld

Hampton Inn & Suites by Hilton San Diego SeaWorld
3.0 star property
3.2 km from Mission Bay
9.2 out of 10, Wonderful, (431)
"Clean rooms, friendly staff."
United States
KARLA
The price is ฿3,177
฿3,652 total
includes taxes & fees
4 Jan - 5 Jan 2026
Hampton Inn & Suites by Hilton San Diego SeaWorld
On the beach
The Beach Cottages

The Beach Cottages

The Beach Cottages
2.5 star property
Pacific Beach, 3.2 km from Mission Bay
9.2 out of 10, Wonderful, (1004)
"Staff was very helpful, place was clean, fun with all the Xmas bars and restaurants."
United States
Gay Marie
The price is ฿3,455
฿3,971 total
includes taxes & fees
23 Dec - 24 Dec
The Beach Cottages
2 outdoor pools, a heated pool, pool loungers
The Dana on Mission Bay

The Dana on Mission Bay

The Dana on Mission Bay
3.5 star property
Mission Bay, 1.7 km from Mission Bay
9.0 out of 10, Wonderful, (3935)
"Always love staying here. Staff was very courteous and the rooms very clean. "
United States
Eric
The price is ฿4,366
฿5,646 total
includes taxes & fees
22 Dec - 23 Dec
The Dana on Mission Bay
Lobby
Fairfield Inn & Suites by Marriott San Diego Pacific Beach

Fairfield Inn & Suites by Marriott San Diego Pacific Beach

Fairfield Inn & Suites by Marriott San Diego Pacific Beach
2.5 star property
Pacific Beach, 2.9 km from Mission Bay
9.0 out of 10, Wonderful, (807)
"good place to stay"
United States
Sisi
The price is ฿3,235
฿3,719 total
includes taxes & fees
30 Dec - 31 Dec
Fairfield Inn & Suites by Marriott San Diego Pacific Beach
Property grounds
Paradise Point Resort & Spa

Paradise Point Resort & Spa

Paradise Point Resort & Spa
4.0 star property
Mission Bay, 1.2 km from Mission Bay
8.8 out of 10, Excellent, (2354)
"Great stay, top tier service and excellent customer care "
Canada
Meriem
The price is ฿4,063
฿6,332 total
includes taxes & fees
11 Jan - 12 Jan 2026
Paradise Point Resort & Spa
Suite, Multiple Beds | In-room safe, desk, laptop workspace, blackout curtains
Holiday Inn Express San Diego - SeaWorld Area by IHG

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
8.8 out of 10, Excellent, (1005)
"Friendly staff at check in and clean room/hotel "
United States
Stefanie
The price is ฿3,989
฿4,585 total
includes taxes & fees
19 Jan - 20 Jan 2026
Holiday Inn Express San Diego - SeaWorld Area by IHG
In-room safe, desk, blackout curtains, iron/ironing board
Bahia Resort Hotel

Bahia Resort Hotel

Bahia Resort Hotel
3.5 star property
Central Mission Beach, 2 km from Mission Bay
8.6 out of 10, Excellent, (1818)
"Friendly staff and beautiful property "
United States
Cherron
The price is ฿3,978
฿6,321 total
includes taxes & fees
4 Jan - 5 Jan 2026
Bahia Resort Hotel
View from room
Catamaran Resort and Spa

Catamaran Resort and Spa

Catamaran Resort and Spa
4.0 star property
Mission Beach, 2.9 km from Mission Bay
8.6 out of 10, Excellent, (1112)
"Great place to vacation. "
United States
Manuel
The price is ฿4,749
฿7,136 total
includes taxes & fees
20 Jan - 21 Jan 2026
Catamaran Resort and Spa
Standard Room, 2 Queen Beds, Non Smoking | In-room safe, desk, laptop workspace, blackout curtains
Comfort Inn Sea World Area

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, (3155)
"good hotel "
United States
Lala
The price is ฿2,670
฿3,069 total
includes taxes & fees
4 Jan - 5 Jan 2026
Comfort Inn Sea World Area
Outdoor pool, open 7:00 AM to 10:00 PM, pool cabanas (surcharge)
San Diego Mission Bay Resort

San Diego Mission Bay Resort

San Diego Mission Bay Resort
4.0 star property
Mission Bay, 1.6 km from Mission Bay
8.4 out of 10, Very good, (1310)
"Room was super clean and updated, location up against the bay was perfect. We really enjoyed our stay and want to come back soon!"
United States
Haley
The price is ฿4,625
฿6,733 total
includes taxes & fees
1 Jan - 2 Jan 2026
San Diego Mission Bay Resort
Exterior
Hyatt Regency Mission Bay Spa and Marina

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, (1575)
"Loved our stay "
United States
Jeremy
The price is ฿4,212
฿6,503 total
includes taxes & fees
4 Jan - 5 Jan 2026
Hyatt Regency Mission Bay Spa and Marina
Outdoor pool
Best Western San Diego Pacific Beach/Mission Bay

Best Western San Diego Pacific Beach/Mission Bay

Best Western San Diego Pacific Beach/Mission Bay
2.5 star property
2.5 km from Mission Bay
8.2 out of 10, Very good, (198)
"Great stay, the staff was very friendly! "
United States
frances
The price is ฿2,138
฿2,458 total
includes taxes & fees
4 Jan - 5 Jan 2026
Best Western San Diego Pacific Beach/Mission Bay
Fishing
Surfer Beach Hotel

Surfer Beach Hotel

Surfer Beach Hotel
3.0 star property
Pacific Beach, 3 km from Mission Bay
8.2 out of 10, Very good, (1184)
"Right on the beach!! Old vintage hotel at a great price. Beds are super comfortable. "
United States
Stacy
The price is ฿3,392
฿3,831 total
includes taxes & fees
22 Dec - 23 Dec
Surfer Beach Hotel
Standard Room, 2 Queen Beds | Pillow-top beds, individually decorated, individually furnished, desk
GreenTree Inn San Diego Mission Bay

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, (1877)
"Good budget room in SD"
United States
John
The price is ฿3,027
฿3,480 total
includes taxes & fees
4 Jan - 5 Jan 2026
GreenTree Inn San Diego Mission Bay
Desk, laptop workspace, blackout curtains, iron/ironing board
SureStay Hotel by Best Western San Diego Pacific Beach

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, (1422)
"our stay was great and staff was supportive..."
United States
Ramesh
The price is ฿2,487
฿2,809 total
includes taxes & fees
4 Jan - 5 Jan 2026
SureStay Hotel by Best Western San Diego Pacific Beach
Sun deck
ITH Beach Bungalow Surf Hostel

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, (254)
"Everyone was so cool and welcoming"
United States
noah
The price is ฿2,714
฿3,060 total
includes taxes & fees
24 Dec - 25 Dec
ITH Beach Bungalow Surf Hostel
Front of property
Heritage Inn San Diego

Heritage Inn San Diego

Heritage Inn San Diego
2.0 star property
2.5 km from Mission Bay
7.4 out of 10, Good, (1171)
"Clean room, great location "
United States
Benjamin
The price is ฿1,625
฿1,868 total
includes taxes & fees
22 Dec - 23 Dec
Heritage Inn San Diego
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.
View all properties

Top Mission Bay Hotel Reviews

The Wayfarer San Diego

The Wayfarer San Diego

10/10 Excellent
"Great room, clean and updated property, exceptional service, perfect location. Loved our stay and can't wait to return. "
Michelle 3-night trip
Posted 17 hours ago
The Wayfarer San Diego

Hotels near other Mission Bay attractions

Mission Bay Park

4.4/5 (165 reviews)
Mission Bay Park is just one of the places to see in San Diego, so why not enjoy the other things to explore during your travels? Discover the beautiful sunsets in this walkable area or enjoy its surfing spots.
See properties

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, take a look at the 44 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 0.7 mi (1.2 km) from Mission Bay. Another good option is San Diego Mission Bay Resort, located just 1 mi (1.6 km) away.
How many hotels will I find near Mission Bay?
Expedia has 44 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.