Beginning of main content

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 (3,548 reviews)
Old World Charm it was like taking a step back in time. The ceilings are unusually high in the room which makes the … - 

$102

$102
The Sofia Hotel

The Sofia Hotel

150 W Broadway, San Diego
4.0 out of 5.0
4.3 out of 5 (7,401 reviews)
There are extra Sophia hotel fees It is well located. Unfortunately, I had to pay an extra $89.75 for 5 day because of the hotel inte … - 

$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 (4,521 reviews)
The location and facilities were just rite We had a great experience and that's what a trip is all about, the hotel room we had was in good sh … - 

$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 (7,067 reviews)
Best Vacation Felt like we were in an oasis, perfect weekend and weather. - 

$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 (1,920 reviews)
Quiet accommodations at a reasonable price. Quiet accommodations at a reasonable price. Minimal breakfast provided in a confined space. Inner c … - 

$62

$62
The Atwood

The Atwood

1201 Hotel Circle South, San Diego
3.5 out of 5.0
3.8 out of 5 (1,099 reviews)
Excellent Hotel Nice and clean hotel. comfortable stay. noise free even being close to highway. wish the pool stay … - 

$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 (1,710 reviews)
LOVE THIS HOTEL! Beautiful location, comfortable and clean rooms, excellent food from room service, nice pool and sp … - 

$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 (2,475 reviews)
Central to beaches and local color. Quite a large resort with wide selection of accommodations from nice bayside views to warm tropical … - 

$129

$129
Urban Boutique Hotel

Urban Boutique Hotel

1654 Columbia Street, San Diego
3.5 out of 5.0
3.9 out of 5 (2,759 reviews)
Nice hotel Very close to several restaurants and some boutique shopping. 7 eleven close by, also. But, it is i … - 

$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 (2,950 reviews)
Historic Hotel, in a good way. This hotel will be one that we go to again when in San Diego. It has a historic feel. The pool and … - 

$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 (1,991 reviews)
Cool location - lowkey Nice place. Good restaurants near by. Staff were friendly for the most part. Worth the money. - 

$99

$99
Viejas Casino & Resort

Viejas Casino & Resort

5000 Willows Road, Alpine
4.5 out of 5.0
4.6 out of 5 (706 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 (1,852 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 (1,814 reviews)
Hotel on the beach If you need to be on the beach, this place is ok. Kind of dated rooms and rooms with outside doors … - 

$229

$229
Porto Vista Hotel

Porto Vista Hotel

1835 Columbia St, San Diego
4.0 out of 5.0
3.4 out of 5 (2,048 reviews)
Convenient to airport and pier. Great location for exploring "little Italy." - 

$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 (1,870 reviews)
Close to Little Italy Staff are great! Friendly and accommodating. This is an older hotel, just a few blocks from the har … - 

$60

$60
Pleasant Inn

Pleasant Inn

5550 Clairemont Mesa Blvd, San Diego
3.0 out of 5.0
4.1 out of 5 (562 reviews)
Nice and cheap hotel at a good location I stayed at Comfort Inn in Gaslamp district for four nights and two night for this one. This one be … - 

$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 (527 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 (3,908 reviews)
The staff here was so incredibly helpful, kind and supportive. They make every effort to make your … - 

$112

$112
Map

Recently booked San Diego County hotels

Best Western Plus Island Palms Hotel & Marina
3.5 out of 5.0
Last booking: 3 minutes ago
Hard Rock Hotel San Diego
4.5 out of 5.0
Last booking: 6 minutes ago
Old Town Western Inn & Suites
3.0 out of 5.0
Last booking: 11 minutes ago
DoubleTree by Hilton San Diego Downtown
3.5 out of 5.0
Last booking: 11 minutes ago
SpringHill Suites by Marriott San Diego Oceanside/Downtown
3.5 out of 5.0
Last booking: 13 minutes ago
The Dana on Mission Bay
4.0 out of 5.0
Last booking: 14 minutes ago
La Valencia Hotel
4.5 out of 5.0
Last booking: 16 minutes ago
Sheraton La Jolla Hotel
4.0 out of 5.0
Last booking: 19 minutes ago
Hotel Indigo Gaslamp Quarter
4.0 out of 5.0
Last booking: 19 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.