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 2,143 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 (3,544 reviews)
Nice stay downtown, great place in the middle of t A whole lot of history very nice bar and the location in great - 

$102

$102
The Sofia Hotel

The Sofia Hotel

150 W Broadway, San Diego
4.0 out of 5.0
4.3 out of 5 (7,397 reviews)
Wonderful Anniversary Stay! Loved the hotel ambiance and my room! Definitely staying here again! - 

$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 (4,517 reviews)
Well cared for resort hotel with excellent views Excellent service and very helpful accommodations for us and our elderly parents. - 

$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 (7,059 reviews)
Great getaway Beautiful view, awesome grounds, great service. Beds were super comfortable room was clean - 

$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 (1,923 reviews)
appears grungy, but actually very adequate inside. - 

$62

$62
The Atwood

The Atwood

1201 Hotel Circle South, San Diego
3.5 out of 5.0
3.8 out of 5 (1,090 reviews)
Excellent Hotel Nice and clean hotel. comfortable stay. noise free even being close to highway. wish the pool stay … - 

$61

$61
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 (1,709 reviews)
Next to Lake San Marcos Great place. Our bed was much harder than expected. Lumpy. Pillows were good. Thanks - 

$77

$77
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)
Excellent location but very outdated I’ve been here several times and love being close to the bay and the beach. However, I’m very disap … - 

$129

$129
Urban Boutique Hotel

Urban Boutique Hotel

1654 Columbia Street, San Diego
3.5 out of 5.0
3.9 out of 5 (2,755 reviews)
It was okay. Quite small, but close to everything. Lots of construction going on nearby. - 

$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 (2,949 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 … - 

$109

$109
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 (1,990 reviews)
Beautiful surroundings. Excellent staff. Clean. Close to Point Loma. Try to book a marina view room … - 

$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 (1,811 reviews)
weekend with grandaughters celebrated a birthday and belated holidays with grandaughters - 

$229

$229
Porto Vista Hotel

Porto Vista Hotel

1835 Columbia St, San Diego
4.0 out of 5.0
3.4 out of 5 (2,045 reviews)
Great Location The Porto Vista was a good experience. The only complaint I would have is the fact that my room was … - 

$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 (1,660 reviews)
close to everything not as bad as some reviews about this hotel but don’t expect much - 

$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 (1,869 reviews)
Nice Central Stay Harborview Inn was very central to everything we wanted to do. It was only a block from Little Ital … - 

$57

$57
Pleasant Inn

Pleasant Inn

5550 Clairemont Mesa Blvd, San Diego
3.0 out of 5.0
4.1 out of 5 (559 reviews)
Clean and cheap room with lots of traffic noise Checked in the evening. The hotel is pretty close to highway and major road unforrunatly. I tgink t … - 

$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 (525 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 (3,905 reviews)
Remarkably friendly staff and convenient access to Legoland for children. They have a shuttle that … - 

$112

$112
Map

Recently booked San Diego County hotels

Days Inn & Suites San Diego SeaWorld/Airport
2.5 out of 5.0
Last booking: 1 minute ago
DoubleTree by Hilton San Diego Downtown
3.5 out of 5.0
Last booking: 9 minutes ago
Motel 6 San Diego - El Cajon
2.5 out of 5.0
Last booking: 14 minutes ago
Days Inn San Diego Hotel Circle Near SeaWorld
3.0 out of 5.0
Last booking: 42 minutes ago
Holiday Inn La Mesa
3.5 out of 5.0
Last booking: 1 hour ago
The Beach Cottages
3.0 out of 5.0
Last booking: 1 hour ago
Staypineapple at Hotel Z
3.0 out of 5.0
Last booking: 1 hour ago
Wyndham San Diego Bayside
4.5 out of 5.0
Last booking: 1 hour ago
Kimpton Hotel Palomar San Diego
5.0 out of 5.0
Last booking: 1 hour 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.