Search Hotels Near Shelter Island, San Diego

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Our top choices for Shelter Island hotels

Exterior
Bay Club Hotel & Marina

Bay Club Hotel & Marina

Bay Club Hotel & Marina
3.5 star property
0.7 km from Shelter Island
9.2 out of 10, Wonderful, (3219)
"Great stay and location!"
United States
Jason
The price is ฿3,464
฿3,981 total
includes taxes & fees
1 Jan - 2 Jan 2026
Bay Club Hotel & Marina
Outdoor pool
Humphreys Half Moon Inn

Humphreys Half Moon Inn

Humphreys Half Moon Inn
3.5 star property
1 km from Shelter Island
9.2 out of 10, Wonderful, (2713)
"Great stay"
United States
Michael
The price is ฿4,624
฿5,936 total
includes taxes & fees
4 Jan - 5 Jan 2026
Humphreys Half Moon Inn
Theatre show
Homewood Suites by Hilton San Diego Airport/Liberty Station

Homewood Suites by Hilton San Diego Airport/Liberty Station

Homewood Suites by Hilton San Diego Airport/Liberty Station
3.0 star property
2.4 km from Shelter Island
9.4 out of 10, Exceptional, (1370)
"Great place to stay at!"
United States
Sandy
The price is ฿4,810
฿5,529 total
includes taxes & fees
5 Jan - 6 Jan 2026
Homewood Suites by Hilton San Diego Airport/Liberty Station
Reception
Best Western Plus Island Palms Hotel & Marina

Best Western Plus Island Palms Hotel & Marina

Best Western Plus Island Palms Hotel & Marina
3.0 star property
0.4 km from Shelter Island
8.8 out of 10, Excellent, (1557)
"Staff was great, easy check in and great location"
United States
Alysa
The price is ฿3,575
฿4,110 total
includes taxes & fees
12 Jan - 13 Jan 2026
Best Western Plus Island Palms Hotel & Marina
Exterior
Hampton Inn & Suites San Diego Airport Liberty Station

Hampton Inn & Suites San Diego Airport Liberty Station

Hampton Inn & Suites San Diego Airport Liberty Station
2.5 star property
2.7 km from Shelter Island
9.2 out of 10, Wonderful, (1710)
"Staff was friendly, room was clean, breakfast very good."
United States
Robert
The price is ฿4,720
฿5,426 total
includes taxes & fees
4 Jan - 5 Jan 2026
Hampton Inn & Suites San Diego Airport Liberty Station
View from property
Courtyard by Marriott San Diego Airport/Liberty Station

Courtyard by Marriott San Diego Airport/Liberty Station

Courtyard by Marriott San Diego Airport/Liberty Station
3.0 star property
2.6 km from Shelter Island
9.2 out of 10, Wonderful, (1363)
"Lovely place to stay!"
United States
Helga
The price is ฿4,778
฿5,493 total
includes taxes & fees
31 Dec - 1 Jan 2026
Courtyard by Marriott San Diego Airport/Liberty Station
BBQ/picnic Area
TownePlace Suites by Marriott San Diego Airport/Liberty Station

TownePlace Suites by Marriott San Diego Airport/Liberty Station

TownePlace Suites by Marriott San Diego Airport/Liberty Station
3.0 star property
2.8 km from Shelter Island
9.0 out of 10, Wonderful, (1000)
"Excellent hotel we stay at from time-to-time because it's close and wakable to airport."
United States
WILLIAM JAMES
The price is ฿5,279
฿6,068 total
includes taxes & fees
4 Jan - 5 Jan 2026
TownePlace Suites by Marriott San Diego Airport/Liberty Station
Front of property
The Pearl Hotel

The Pearl Hotel

The Pearl Hotel
4.0 star property
1.6 km from Shelter Island
8.8 out of 10, Excellent, (1004)
"Lovely spot would stay again "
United States
danixa
The price is ฿3,561
฿4,022 total
includes taxes & fees
4 Jan - 5 Jan 2026
The Pearl Hotel
Desk, blackout curtains, iron/ironing board, cots/infant beds
Best Western Yacht Harbor Hotel

Best Western Yacht Harbor Hotel

Best Western Yacht Harbor Hotel
2.5 star property
1.7 km from Shelter Island
8.6 out of 10, Excellent, (1649)
"Enjoyed our stay. Very nice staff!"
United States
Julia
The price is ฿3,476
฿3,989 total
includes taxes & fees
4 Jan - 5 Jan 2026
Best Western Yacht Harbor Hotel
Exterior
Hilton San Diego Airport/Harbor Island

Hilton San Diego Airport/Harbor Island

Hilton San Diego Airport/Harbor Island
3.5 star property
2.5 km from Shelter Island
8.8 out of 10, Excellent, (1225)
"Clean and spacious rooms, wonderful bar on the bay, great place to see Christmas boat parade, friendly staff."
United States
Jessica or Ian
The price is ฿5,064
฿5,821 total
includes taxes & fees
3 Jan - 4 Jan 2026
Hilton San Diego Airport/Harbor Island
Property amenity
The Monsaraz San Diego, Tapestry Collection by Hilton

The Monsaraz San Diego, Tapestry Collection by Hilton

The Monsaraz San Diego, Tapestry Collection by Hilton
3.5 star property
1.6 km from Shelter Island
8.6 out of 10, Excellent, (630)
"Staff, room cleanliness, location all excellent! I definitely hope to be back soon!"
United States
Wesley
The price is ฿3,699
฿4,252 total
includes taxes & fees
5 Jan - 6 Jan 2026
The Monsaraz San Diego, Tapestry Collection by Hilton
Marina
Sea Harbor Hotel

Sea Harbor Hotel

Sea Harbor Hotel
2.0 star property
1.4 km from Shelter Island
8.4 out of 10, Very good, (1005)
"Great stay"
United States
Naomi
Sea Harbor Hotel
2 outdoor pools, open 6:00 AM to 10:00 PM, pool cabanas (surcharge)
Kona Kai San Diego

Kona Kai San Diego

Kona Kai San Diego
4.0 star property
0.2 km from Shelter Island
8.2 out of 10, Very good, (1003)
"had a wonderful time for our honey moon here "
United States
Anna
The price is ฿5,558
฿8,251 total
includes taxes & fees
4 Jan - 5 Jan 2026
Kona Kai San Diego
Golf
DoubleTree by Hilton San Diego Bayside

DoubleTree by Hilton San Diego Bayside

DoubleTree by Hilton San Diego Bayside
3.0 star property
1.8 km from Shelter Island
8.2 out of 10, Very good, (1003)
" food by the pool was good and bartender was friendly and fast"
United States
manirath
The price is ฿3,537
฿4,066 total
includes taxes & fees
3 Jan - 4 Jan 2026
DoubleTree by Hilton San Diego Bayside
Exterior
Comfort Inn San Diego Airport At The Harbor

Comfort Inn San Diego Airport At The Harbor

Comfort Inn San Diego Airport At The Harbor
3.5 star property
1.6 km from Shelter Island
7.8 out of 10, Good, (1213)
"Convenient location and friendly staff."
United States
Justin
The price is ฿2,828
฿3,194 total
includes taxes & fees
27 Jan - 28 Jan 2026
Comfort Inn San Diego Airport At The Harbor
In-room safe, individually decorated, individually furnished, desk
Ramada by Wyndham San Diego Airport

Ramada by Wyndham San Diego Airport

Ramada by Wyndham San Diego Airport
3.0 star property
1.6 km from Shelter Island
7.4 out of 10, Good, (1003)
"Close to airport and the water, free on site parking."
United States
Christina
The price is ฿2,928
฿3,360 total
includes taxes & fees
4 Jan - 5 Jan 2026
Ramada by Wyndham San Diego Airport
Suite, 1 Queen Bed with Sofa bed, Kitchenette | Blackout curtains, iron/ironing board, free WiFi, bed sheets
Hotel Point Loma

Hotel Point Loma

Hotel Point Loma
2.0 star property
1.5 km from Shelter Island
7.4 out of 10, Good, (354)
"Great staff and very friendly "
United States
Nalani
Hotel Point Loma
Front of property
Sunrise Inn San Diego

Sunrise Inn San Diego

Sunrise Inn San Diego
2.0 star property
1.2 km from Shelter Island
5.6 out of 10, (1003)
"For the price and location this hotel is great. My go to when I’m down in San Diego and don’t want to break the bank "
United States
carmina
Sunrise Inn San Diego
Bed In 8-Bed Dorm | Free WiFi, bed sheets
Samesun Ocean Beach - Hostel

Samesun Ocean Beach - Hostel

Samesun Ocean Beach - Hostel
2.0 star property
Ocean Beach, 4.3 km from Shelter Island
9.6 out of 10, Exceptional, (378)
"My stay was awesome"
United States
Fred
Samesun Ocean Beach - Hostel
Property grounds
The Inn at Sunset Cliffs

The Inn at Sunset Cliffs

The Inn at Sunset Cliffs
2.5 star property
Ocean Beach, 3.6 km from Shelter Island
9.2 out of 10, Wonderful, (1007)
"Great place beautiful view "
United States
Josue
The price is ฿6,083
฿6,859 total
includes taxes & fees
30 Dec - 31 Dec
The Inn at Sunset Cliffs
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.
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Top Shelter Island Hotel Reviews

The Monsaraz San Diego, Tapestry Collection by Hilton

The Monsaraz San Diego, Tapestry Collection by Hilton

10/10 Excellent
"Staff courteous, very beautiful entry, room was perfect. "
Lydia 2-night trip
Posted 6 days ago
The Monsaraz San Diego, Tapestry Collection by Hilton
Kona Kai San Diego

Kona Kai San Diego

10/10 Excellent
"Room nicely appointed. Great view of boats. Service and food at conference was very good. I had a very enjoyable stay"
Barbara 2-night trip
Posted 2 months ago
Kona Kai San Diego

Hotels near other Shelter Island attractions

Sunset Cliffs Natural Park, San Diego, California

Sunset Cliffs Natural Park

You can take time to visit Sunset Cliffs Natural Park during your travels to San Diego. Wander the seaside and beautiful beaches in the area.
See properties
Favorite sunset
Photo by Bikini Traveler
Open Photo by Bikini Traveler

Breakers Beach

Why not spend a lazy afternoon at Breakers Beach during your trip to San Diego? Experience the acclaimed theatre scene and entertainment choices in this walkable area.
See properties

Frequently asked questions

What's the area like around Shelter Island?
Shelter Island is located in a family-friendly area of San Diego known for its beautiful island views and great live music scene. 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 Shelter Island?
Adjacent to Shelter Island, Best Western Plus Island Palms Hotel & Marina is one of the top choices for your stay based on our traveller data, and this hotel offers a marina and 2 outdoor pools. Other good choices within a short distance include Bay Club Hotel & Marina and Kona Kai San Diego.
How many hotels will I be able to find near Shelter Island?
Expedia has 44 hotels and other accommodation options within a mile from Shelter Island.
If I need to cancel the hotel reservation for my stay near Shelter Island, will I receive a refund?
Yes! Most hotel room reservations are fully refundable if cancelled before the accommodation's cancellation deadline, which in most cases is within 24 or 48 hours of your arrival date. If you booked a non-refundable reservation, you might still have the option to cancel and get a refund within 24 hours of your booking. Add dates, click "Search", then you can use the "fully refundable" filter to get the best deals near Shelter Island.
What can I see and do near Shelter Island?
You might want to spend some time browsing the exhibits at USS Midway Museum, Maritime Museum of San Diego or San Diego Air and Space Museum. Explore notable local landmarks like Hotel del Coronado, Point Loma Lighthouse and Star of India. You can check out the local talent at Humphreys Concerts by the Bay, The Rady Shell at Jacobs Park and San Diego Civic Theatre.