Search Hotels Near Shelter Island, San Diego

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30 Dec - 31 Dec
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2 Jan - 4 Jan
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9 Jan - 11 Jan

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Our top choices for Shelter Island hotels

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, (1366)
"Great place to stay at!"
United States
Sandy
The price is ฿5,187
฿5,962 total
includes taxes & fees
10 Jan - 11 Jan 2026
Homewood Suites by Hilton San Diego Airport/Liberty Station
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, (3234)
"Great stay and location!"
United States
Jason
The price is ฿3,390
฿3,896 total
includes taxes & fees
4 Jan - 5 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, (2727)
"Great stay, highly recommend."
United States
Ryan
The price is ฿4,687
฿6,017 total
includes taxes & fees
1 Jan - 2 Jan 2026
Humphreys Half Moon Inn
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, (1716)
"Staff was friendly, room was clean, breakfast very good."
United States
Robert
The price is ฿4,814
฿5,533 total
includes taxes & fees
6 Jan - 7 Jan 2026
Hampton Inn & Suites 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, (1004)
"Excellent hotel we stay at from time-to-time because it's close and wakable to airport."
United States
WILLIAM JAMES
The price is ฿4,785
฿5,500 total
includes taxes & fees
16 Jan - 17 Jan 2026
TownePlace Suites by Marriott 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, (1561)
"Staff was great, easy check in and great location"
United States
Alysa
The price is ฿3,699
฿4,252 total
includes taxes & fees
14 Jan - 15 Jan 2026
Best Western Plus Island Palms Hotel & Marina
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, (1226)
"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 ฿5,133
฿5,900 total
includes taxes & fees
6 Jan - 7 Jan 2026
Hilton San Diego Airport/Harbor Island
Marina
Sea Harbor Hotel

Sea Harbor Hotel

Sea Harbor Hotel
2.0 star property
1.4 km from Shelter Island
8.6 out of 10, Excellent, (1010)
"Great stay"
United States
Naomi
Sea Harbor 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, (1651)
"Enjoyed our stay. Very nice staff!"
United States
Julia
The price is ฿3,523
฿4,043 total
includes taxes & fees
4 Jan - 5 Jan 2026
Best Western Yacht Harbor Hotel
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, (631)
"Staff, room cleanliness, location all excellent! I definitely hope to be back soon!"
United States
Wesley
The price is ฿3,906
฿4,490 total
includes taxes & fees
11 Jan - 12 Jan 2026
The Monsaraz San Diego, Tapestry Collection by Hilton
Front of property
The Pearl Hotel

The Pearl Hotel

The Pearl Hotel
4.0 star property
1.6 km from Shelter Island
8.6 out of 10, Excellent, (1003)
"Lovely spot would stay again "
United States
danixa
The price is ฿3,610
฿4,077 total
includes taxes & fees
12 Jan - 13 Jan 2026
The Pearl 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, (1004)
"had a wonderful time for our honey moon here "
United States
Anna
The price is ฿5,517
฿8,240 total
includes taxes & fees
11 Jan - 12 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, (1002)
" food by the pool was good and bartender was friendly and fast"
United States
manirath
The price is ฿4,047
฿4,652 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, (1219)
"good place to stay at! comfortable and the workers are very nice. "
United States
Litzy
The price is ฿2,884
฿3,258 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, (1006)
"Very pleasent reception staff. "
United States
Anil S V
The price is ฿2,874
฿3,297 total
includes taxes & fees
6 Jan - 7 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, (355)
"Great staff and very friendly "
United States
Nalani
Hotel Point Loma
Front of property – evening/night
Hotel Aqua Mar

Hotel Aqua Mar

Hotel Aqua Mar
2.0 star property
1.7 km from Shelter Island
6.4 out of 10, (1000)
"A/C / Heat works great!"
United States
Candice
Hotel Aqua Mar
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, (1002)
"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, (382)
"My stay was awesome"
United States
Fred
Samesun Ocean Beach - Hostel
Beach nearby, beach umbrellas, beach towels
1906 Lodge

1906 Lodge

1906 Lodge
3.5 star property
5.9 km from Shelter Island
9.8 out of 10, Exceptional, (889)
"Absolutely love the attention to the small things that make this place so special "
United States
Rhandy
The price is ฿7,833
฿8,632 total
includes taxes & fees
14 Jan - 15 Jan 2026
1906 Lodge
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 8 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.
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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 45 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, Kona Kai San Diego 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 Best Western Plus Island Palms Hotel & Marina.
How many hotels will I be able to find near Shelter Island?
Expedia has 45 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.