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Featured Mission Bay Independent Hotels

See all 274 Hotels in Mission Bay
Paradise Point Resort & Spa

Paradise Point Resort & Spa

1404 Vacation Rd, San Diego
4.5 out of 5.0
3.7 out of 5 (2,279 reviews)
Wonderful place by mission bay Great views of mission bay and wonderful dinning options at the hotel. - 

$104

$104
Bahia Resort Hotel

Bahia Resort Hotel

998 W Mission Bay Dr, San Diego
4.0 out of 5.0
4.1 out of 5 (4,445 reviews)
Amazing They thought of everything! Awesome hotel! Wonderful views as well! - 

$99

$99
The Dana on Mission Bay

The Dana on Mission Bay

1710 W Mission Bay Dr, San Diego
4.0 out of 5.0
4.1 out of 5 (7,021 reviews)
Nice hotel very convenient We stayed for 5 days and really enjoyed the hotel. Excellent rooms, excellent staff and facilities … - 

$95

$95
Catamaran Resort and Spa

Catamaran Resort and Spa

3999 Mission Boulevard, San Diego
4.5 out of 5.0
4.2 out of 5 (2,468 reviews)
Close to beach and Amenities Not bad for the money however we were right next to the elevator bad Room. bathtub faucet had a hea … - 

$129

$129
Hyatt Regency Mission Bay Spa and Marina

Hyatt Regency Mission Bay Spa and Marina

1441 Quivira Rd, San Diego
4.5 out of 5.0
3.9 out of 5 (2,828 reviews)
38 dollar parking Room + resort fee + $38 dollar parking, it adds up. place is beautiful though. My girls love it. - 

$85

$85
Red Roof Inn San Diego - Pacific Beach/SeaWorld Area

Red Roof Inn San Diego - Pacific Beach/SeaWorld Area

4545 Mission Bay Dr, San Diego
2.0 out of 5.0
3.2 out of 5 (1,090 reviews)
Clean modest room for my visits to San Diego The rooms are modest but very pleasing and efficient. The staff treated me well. I like having both … - 

$64

$64
La Quinta Inn & Suites San Diego Mission Bay

La Quinta Inn & Suites San Diego Mission Bay

4610 De Soto St, San Diego
3.5 out of 5.0
3.8 out of 5 (1,072 reviews)
Good location. Parking spaces a bit small but we were always able to find a more isolated spot. It … - 

$79

$79
Holiday Inn Express San Diego Sea World - Beach Area

Holiday Inn Express San Diego Sea World - Beach Area

4540 Mission Bay Drive, San Diego
3.0 out of 5.0
4.0 out of 5 (931 reviews)
Clean hotel, good breakfast & easy check in Room was clean, updated, and bed was super comfortable. TV options were good. Bed was extremely com … - 

$86

$86
Rodeway Inn San Diego Beach SeaWorld Area

Rodeway Inn San Diego Beach SeaWorld Area

4345 Mission Bay Dr, San Diego
2.5 out of 5.0
3.5 out of 5 (830 reviews)
Late night arrival - had to wait in empty lobby for attendant - 

$51

$51
Motel San Diego

Motel San Diego

4780 Mission Bay Dr, San Diego
2.5 out of 5.0
2.0 out of 5 (38 reviews)
Basic motel A very basic motel with no frills just off freeway - 

$51

$51
Mission Beach Townhouse by RedAwning

Mission Beach Townhouse by RedAwning

715-B Asbury Ct, San Diego
4.5 out of 5.0
Pet Friendly Bayside Studio With Kingsize Bed, Kitchenette and Beach Cruisers!

Pet Friendly Bayside Studio With Kingsize Bed, Kitchenette and Beach Cruisers!

3038 glendora street, san diego
4.7 out of 5 (28 reviews)
Mike s Place at the Beach

Mike s Place at the Beach

718 Jamaica Court, San Diego
4.0 out of 5.0
Reduced Price FOR 2017 30 Steps to Beach Views of Pacific Ocean, Mission Bay

Reduced Price FOR 2017 30 Steps to Beach Views of Pacific Ocean, Mission Bay

725 Redondo Ct, San Diego
4.8 out of 5 (46 reviews)
Sangabrie l727 Condo by RedAwning

Sangabrie l727 Condo by RedAwning

727 San Gabriel Pl, San Diego
4.0 out of 5.0
3BR 3BA Mission Beach Home by RedAwning

3BR 3BA Mission Beach Home by RedAwning

810 Ensenada Court, San Diego
3.5 out of 5.0
2 Bedroom Townhome 2 Mins. to the Beach

2 Bedroom Townhome 2 Mins. to the Beach

823 Nantasket Ct, San Diego
4.0 out of 5.0
3.6 out of 5 (5 reviews)
Kennebeck 729 Townhome by RedAwning

Kennebeck 729 Townhome by RedAwning

729 Kennebeck Ct, San Diego
4.0 out of 5.0
Can't get any Closer to the Sand! Huge Patio/sunsets/fun & Sun!

Can't get any Closer to the Sand! Huge Patio/sunsets/fun & Sun!

3405 Ocean Front Walk, San Diego
5.0 out of 5 (14 reviews)
20%discounted! Best Location! 1 House From Ocean. Charming, Clean

20%discounted! Best Location! 1 House From Ocean. Charming, Clean

716 Jersey Court, San Diego
4.8 out of 5 (10 reviews)
Map

Recently booked Mission Bay hotels

Bahia Resort Hotel
4.0 out of 5.0
Last booking: 3 hours ago
The Dana on Mission Bay
4.0 out of 5.0
Last booking: 6 hours ago
Paradise Point Resort & Spa
4.5 out of 5.0
Last booking: 10 hours ago
Catamaran Resort and Spa
4.5 out of 5.0
Last booking: 10 hours ago
Hilton San Diego Resort & Spa
4.5 out of 5.0
Last booking: 10 hours ago
Hyatt Regency Mission Bay Spa and Marina
4.5 out of 5.0
Last booking: 12 hours ago
La Quinta Inn & Suites San Diego Mission Bay
3.5 out of 5.0
Last booking: 12 hours ago
Red Roof Inn San Diego - Pacific Beach/SeaWorld Area
2.0 out of 5.0
Last booking: 13 hours ago
Rodeway Inn San Diego Beach SeaWorld Area
2.5 out of 5.0
Last booking: 15 hours ago

Independent Mission Bay Hotel Guide

Some globe-trotters choose hotels based on location, but others book by name. And thanks to Expedia you don’t have to pick. It is why we offer such an expansive range of Independent hotels in Mission Bay, San Diego. Known for well-appointed rooms and friendly, personalized service, each of the top Independent Mission Bay hotels guarantees an unparalleled level of comfort and quality.

You’ll find best-in-class amenities like clean rooms and quiet atmospheres, and some Mission Bay Independent locations may even offer extra little benefits and discounts for frequent travelers.