Search Hotels Near Shelter Island, San Diego

Start date: Check-in selected.
To Date
End date: Check-out

  • Change your mind

    Book hotels with free cancellation

  • Treat yourself

    Sign in to save 10% or more on thousands of hotels
    Sign in

  • Be picky

    Search almost a million properties worldwide

Check prices for these dates

Tonight
13 Dec - 14 Dec
Tomorrow
14 Dec - 15 Dec
Next weekend
19 Dec - 21 Dec
In two weeks
26 Dec - 28 Dec

Filter by

Guest rating
Guest rating
Star rating

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, (1354)
"Great place to stay at!"
United States
Sandy
The price is ฿4,993
฿5,739 total
includes taxes & fees
4 Jan - 5 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, (3183)
"Great stay and location!"
United States
Jason
The price is ฿3,918
฿4,504 total
includes taxes & fees
14 Dec - 15 Dec
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, (2693)
"Great stay !!"
United States
Caleb Scott
The price is ฿4,701
฿6,034 total
includes taxes & fees
14 Dec - 15 Dec
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, (1699)
"Excellent place "
Mexico
Rafael
The price is ฿4,265
฿4,903 total
includes taxes & fees
20 Dec - 21 Dec
 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, (1367)
"Lovely place to stay!"
United States
Helga
The price is ฿4,577
฿5,261 total
includes taxes & fees
21 Dec - 22 Dec
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, (1001)
"Great place to stay! Breakfast was fantastic every day."
United States
Mandy
The price is ฿5,082
฿5,842 total
includes taxes & fees
19 Dec - 20 Dec
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, (1554)
"Every time i have stayed here everything is always clean...no complaints!"
United States
Joseline
The price is ฿3,609
฿4,148 total
includes taxes & fees
4 Jan - 5 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, (1223)
"Great hotel"
United States
Maria G
The price is ฿5,148
฿5,917 total
includes taxes & fees
25 Dec - 26 Dec
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, (1001)
"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, (1634)
"The breakfast options were good and the staff were very helpful."
Canada
Gail or Rob
The price is ฿3,095
฿3,552 total
includes taxes & fees
14 Dec - 15 Dec
Best Western Yacht Harbor Hotel
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, (1005)
"Lovely spot would stay again "
United States
danixa
The price is ฿4,344
฿4,907 total
includes taxes & fees
4 Jan - 5 Jan 2026
The Pearl 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, (616)
"Great staff, was able to get checked in about an hour early…. Very nice property, lots of seating areas , outdoor patios …. Great Stay"
United States
Jude
The price is ฿4,013
฿4,613 total
includes taxes & fees
21 Dec - 22 Dec
The Monsaraz San Diego, Tapestry Collection by Hilton
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, (1000)
"had a wonderful time for our honey moon here "
United States
Anna
The price is ฿4,749
฿7,352 total
includes taxes & fees
10 Jan - 11 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, (1004)
"Clean room and lobby, friendly staff, great menu in on-site cafe, convenient shuttles. "
United States
TobiElizabeth
The price is ฿3,984
฿4,579 total
includes taxes & fees
19 Dec - 20 Dec
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, (1183)
"Great location on the bay and close to the airport "
United States
Shawn
The price is ฿2,631
฿2,971 total
includes taxes & fees
5 Jan - 6 Jan 2026
Comfort Inn San Diego Airport At The Harbor
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, (344)
"Aside from the AMAZING staff, the clean rooms, and the great location.. they were extremely accommodating for my recent stay straight out of the hospital and with my service dog. I’ve stayed there before and will most definitely stay there again as long as they have vacancy. 10/10 recommend this place! "
United States
Jamina
Hotel Point Loma
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, (1004)
"Close to airport and the water, free on site parking."
United States
Christina
The price is ฿2,811
฿3,226 total
includes taxes & fees
14 Dec - 15 Dec
Ramada by Wyndham San Diego Airport
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, (1001)
"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, (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, (371)
"My stay was awesome"
United States
Fred
Samesun Ocean Beach - Hostel
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.
View all properties

Top Shelter Island Hotel Reviews

New Cozy Studio 2 Queen Beds, Kitchen Walk to Water

New Cozy Studio 2 Queen Beds, Kitchen Walk to Water

8/10 Good
"The studio was beautiful, clean, and cozy. The only thing that I will say is that the pictures advertised show both the main home and the studio, so it is misleading as to what amenities are available in your own space. Other than that I enjoyed my stay and the owner was very prompt to respond to the few questions that I had."
Fatimah 4-night trip
Posted 5 days ago
New Cozy Studio 2 Queen Beds, Kitchen Walk to Water

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.

Explore a world of travel with Expedia