Beginning of main content
Trip Type
Flight 1
Flight 2
Flight 3
Flight 4
Flight 5

Search 321,000 hotels worldwide.

Get the best price available for your trip.

No Expedia cancellation fee to change or cancel almost any hotel reservation.


Featured San Diego County Independent Hotels

See all 2,109 Hotels in San Diego County
The Horton Grand Hotel

The Horton Grand Hotel

311 Island Ave, San Diego
4.0 out of 5.0
4.3 out of 5 (3,554 reviews)
Great for travelers and couples This hotel is priced well with a great restaurant and amenities. It is very close to the convention … - 

$102

$102
The Sofia Hotel

The Sofia Hotel

150 W Broadway, San Diego
4.0 out of 5.0
4.3 out of 5 (7,411 reviews)
Great location I felt the location was great. Lots of things in walking distance! My only negative about the hotel … - 

$125

$125
Bahia Resort Hotel

Bahia Resort Hotel

998 W Mission Bay Dr, San Diego
4.0 out of 5.0
4.1 out of 5 (4,525 reviews)
Overall, we had a great experience! We had a decent room. We were upset at first because the pictures on Expedia made the hotel look fa … - 

$139

$139
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 (7,077 reviews)
Nice Hotel in a good area The hotel was clean and the staff was friendly. It is in a good area that is close to all of the ma … - 

$79

$79
California Suites Hotel

California Suites Hotel

5415 Clairemont Mesa Blvd, San Diego
2.5 out of 5.0
3.3 out of 5 (1,924 reviews)
Not too bad free breakfast the rooms could have been better - 

$62

$62
The Atwood

The Atwood

1201 Hotel Circle South, San Diego
3.5 out of 5.0
3.8 out of 5 (1,108 reviews)
Good for the price, some ware and tear in room but nice hardwood floors and clean overall. Front de … - 

$59

$59
Lakehouse Hotel and Resort

Lakehouse Hotel and Resort

1025 La Bonita Drive, San Marcos
4.5 out of 5.0
4.6 out of 5 (1,718 reviews)
Absolutely Breathtaking! The Lakehouse Hotel & Resort is an amazing oasis right on the lake. If you get a chance, upgrade to … - 

$119

$119
Catamaran Resort and Spa

Catamaran Resort and Spa

3999 Mission Boulevard, San Diego
4.5 out of 5.0
4.2 out of 5 (2,478 reviews)
Good location, Nice grounds Great location near plenty of restaurants, convenience stores and a grocery store. Beach is only li … - 

$159

$159
Urban Boutique Hotel

Urban Boutique Hotel

1654 Columbia Street, San Diego
3.5 out of 5.0
3.9 out of 5 (2,763 reviews)
Location is great and you are able to walk all around Little Italy and enjoy San Diego. It is like … - 

$84

$84
The Lafayette Hotel, Swim Club & Bungalows

The Lafayette Hotel, Swim Club & Bungalows

2223 El Cajon Blvd, San Diego
3.5 out of 5.0
3.9 out of 5 (2,952 reviews)
Loved the Vibe We ended up booking our room the day of, and to our surprise they upgraded us to a poolside room fo … - 

$115

$115
Bay Club Hotel & Marina

Bay Club Hotel & Marina

2131 Shelter Island Dr, San Diego
4.0 out of 5.0
4.2 out of 5 (1,995 reviews)
Nice hotel across from the bay Got to watch the naval ships coming and going. Older hotel but has been updated recently. Had a cou … - 

$99

$99
Viejas Casino & Resort

Viejas Casino & Resort

5000 Willows Road, Alpine
4.5 out of 5.0
4.6 out of 5 (708 reviews)
Great staff at Viejas I usually don't write good reviews for great customer service has been hard to come by. Working in … - 

$120

$120
Gaslamp Plaza Suites

Gaslamp Plaza Suites

520 E St, San Diego
4.0 out of 5.0
4.1 out of 5 (1,853 reviews)
Perfect spot next to the bars and clubs I loved the decor and the location of the hotel. The window are thin and even with them shut you ca … - 

$99

$99
La Jolla Shores Hotel

La Jolla Shores Hotel

8110 Camino Del Oro, La Jolla
3.5 out of 5.0
4.2 out of 5 (1,819 reviews)
Nice beach hotel Stayed in a beachfront room, lovely to wake up to views of the beach and early morning surfers. Gre … - 

$229

$229
Porto Vista Hotel

Porto Vista Hotel

1835 Columbia St, San Diego
4.0 out of 5.0
3.4 out of 5 (2,051 reviews)
Small but nice room with a bed, desk, TV, chair and small refrigerator. The bed was comfortable but … - 

$111

$111
Bay Inn and Suites at Seaworld

Bay Inn and Suites at Seaworld

3325 Midway Dr, San Diego
2.5 out of 5.0
2.7 out of 5 (1,661 reviews)
The kind lady who checked me in was helpful and efficient. The room is simple but provides everythi … - 

$42

$42
Harborview Inn & Suites San Diego Harbor

Harborview Inn & Suites San Diego Harbor

550 West Grape St, San Diego
2.5 out of 5.0
2.9 out of 5 (1,873 reviews)
Very close to the beach I was satisfied with the room even though I wasn't in there long. Walking distance to both the beac … - 

$60

$60
Pleasant Inn

Pleasant Inn

5550 Clairemont Mesa Blvd, San Diego
3.0 out of 5.0
4.1 out of 5 (565 reviews)
Clean room, really great stay The room was clean the fridge worked fine. Staff was friendly. Good area near amenities. Zero compl … - 

$72

$72
E-Z 8 Motel Old Town

E-Z 8 Motel Old Town

4747 Pacific Highway, San Diego
3.0 out of 5.0
3.0 out of 5 (531 reviews)
Everything is ok, match the price The price is cheap, but the room is not bad, you get what you pay. - 

$45

$45
Carlsbad By The Sea Resort

Carlsbad By The Sea Resort

850 Palomar Airport Road, Carlsbad
3.5 out of 5.0
3.8 out of 5 (3,911 reviews)
Nice hotel near ocean The staff of CBS were prompt and courteous with our requests. Our first room upon arrival had a wet … - 

$112

$112
Map

Recently booked San Diego County hotels

San Diego Marriott La Jolla
0.0 out of 5.0
Last booking: 4 minutes ago
Travelodge El Cajon
2.5 out of 5.0
Last booking: 4 minutes ago
Country Inn & Suites by Carlson-San Diego North
3.5 out of 5.0
Last booking: 5 minutes ago
Hotel Iris - San Diego
3.0 out of 5.0
Last booking: 7 minutes ago
Sheraton Carlsbad Resort & Spa
4.5 out of 5.0
Last booking: 10 minutes ago
Best Western Plus Marina Gateway Hotel
3.5 out of 5.0
Last booking: 11 minutes ago
Residence Inn By Marriott San Diego Central
3.5 out of 5.0
Last booking: 12 minutes ago
Cape Rey Carlsbad, a Hilton Resort
4.5 out of 5.0
Last booking: 12 minutes ago
Omni San Diego Hotel
4.5 out of 5.0
Last booking: 16 minutes ago

Independent San Diego County 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 San Diego County, California. Known for well-appointed rooms and friendly, personalized service, each of the top Independent San Diego County hotels guarantees an unparalleled level of comfort and quality.

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