San Diego Shelter Island Hotels: 2026 Limited-Time Hotel Deals @Expedia

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Our top choices for Shelter Island hotels

A spacious lobby with a large seating area, a wooden ceiling, and large windows offering a view of the outdoor patio area.

A modern lobby with wooden ceiling beams, comfortable seating with yellow cushions, a large wooden coffee table, and large windows offering a view of palm trees and a sunset.

A spacious hotel lobby with a mix of seating arrangements, including a sofa, round tables, and chairs.

An outdoor seating area with tables and chairs, umbrellas, and a fire feature.

1. Hampton Inn & Suites San Diego Airport Liberty Station

2.7 km from Shelter Island

MANUEL

HK$1,281

HK$1,472 total

includes taxes & fees

8 Nov - 9 Nov

A hotel complex with multiple buildings, a landscaped garden, and a body of water reflecting the sunset.

A beach with sand dunes and a person walking.

A pool area with lounge chairs, a palm tree, and a view of a bridge and buildings in the background.

A modern kitchen area with wooden cabinets, marble countertops, and a central island with plates.

2. Homewood Suites by Hilton San Diego Airport/Liberty Station

2.4 km from Shelter Island

Carl

HK$1,435

HK$1,649 total

includes taxes & fees

27 Oct - 28 Oct

A hotel courtyard with outdoor seating, palm trees, and a view of the sea.

A Courtyard by Marriott hotel with a well-lit courtyard, outdoor seating, and a view of the surrounding area.

A modern lobby with a reception desk, seating area, and a large screen.

A bar area with multiple seating options, a well-stocked bar, and a television screen.

3. Courtyard by Marriott San Diego Airport/Liberty Station

2.6 km from Shelter Island

Jaycie Nicole

HK$1,460

HK$1,678 total

includes taxes & fees

1 Nov - 2 Nov

A resort with two-story buildings, balconies, and a pool area.

An outdoor bar area with a pool, bar stools, and a variety of bottles.

A restaurant with a view of a marina, featuring high ceilings, modern lighting, and a central chandelier.

A canal lined with palm trees and a row of buildings with balconies.

4. Humphreys Half Moon Inn

1 km from Shelter Island

Svenja

HK$1,326

HK$1,682 total

includes taxes & fees

16 Nov - 17 Nov

A modern building with a sloped roof and large windows, surrounded by palm trees and a well-maintained garden.

An outdoor patio with round tables and chairs, large umbrellas, and a marina view in the background.

A spacious lobby with a high ceiling, stone flooring, and wicker furniture.

A hotel entrance with a modern design, palm trees, and a sign indicating it is part of the Best Western Plus chain.

5. Best Western Plus Island Palms Hotel & Marina

0.4 km from Shelter Island

Sarah

HK$1,021

HK$1,173 total

includes taxes & fees

17 Nov - 18 Nov

A dining table set with plates, glasses, and a bottle of wine, overlooking a marina with boats.

A conference room with a long table, chairs, and various amenities like a coffee station and a clock on the wall.

A hotel hallway with carpeted floors, recessed lighting, and a central light fixture.

A hotel room with two beds, a desk, a TV, and a mirror.

6. Hilton San Diego Airport/Harbor Island

2.5 km from Shelter Island

Amos

HK$1,281

HK$1,472 total

includes taxes & fees

8 Nov - 9 Nov

A spacious lounge area with a high ceiling, a fireplace, and large windows offering a view of the outdoors.

A spacious hotel lobby with a geometric patterned carpet, leather armchairs, a sofa, and a dining table. Large windows offer views of the outside.

An outdoor seating area with sofas, chairs, and umbrellas, surrounded by buildings.

A modern aquarium with a celestial-themed backdrop.

7. TownePlace Suites by Marriott San Diego Airport/Liberty Station

2.8 km from Shelter Island

Chase

HK$1,335

HK$1,534 total

includes taxes & fees

9 Nov - 10 Nov

A building with a sign reading "the Pearl" and a modern architectural style.

A bathroom with a wooden bench, a mirror, shelves with toiletries, and a robe hanging on the wall.

A poolside area with a bar and outdoor seating, surrounded by a building with a balcony and string lights.

A modern bedroom with a bed, a TV mounted on the wall, and a window with curtains.

8. The Pearl Hotel

1.6 km from Shelter Island

Jane

HK$1,231

HK$1,390 total

includes taxes & fees

25 Oct - 26 Oct

A square pizza on a wooden board with a fire pit in the background.

A spacious indoor dining area with high ceilings, wooden beams, and a mix of booth and table seating.

A hotel with a well-maintained lawn, palm trees, and a pool area.

9. DoubleTree by Hilton San Diego Bayside

1.8 km from Shelter Island

Thomas

HK$1,216

HK$1,398 total

includes taxes & fees

27 Oct - 28 Oct

A hotel room with two beds, a desk, a chair, and a large window with a view of the outdoors.

A hotel room with two beds, a desk, and a chair.

A modern hotel room with a blue sofa, a grey armchair, a round coffee table, and a large window offering a view of the outdoors.

A modern kitchen with a coffee station, a dining area with a large table and chairs, and a carpeted floor.

10. Best Western Yacht Harbor Hotel

1.7 km from Shelter Island

Falizity

HK$895

HK$1,027 total

includes taxes & fees

10 Nov - 11 Nov

A well-lit retail area with shelves displaying various products, a poolside view, and a palm tree.

A modern hotel lobby with white furniture, wooden flooring, and a reception desk.

A modern, well-lit room with a dining area, kitchenette, and a large window offering a city view.

A marina filled with numerous boats, a distant city skyline, and a clear blue sky.

11. Sea Harbor Hotel

1.4 km from Shelter Island

Michael

HK$778

HK$878 total

includes taxes & fees

10 Nov - 11 Nov

An outdoor patio area with seating arrangements, a fire feature, and ambient lighting.

A hotel room with a large TV mounted on a wooden panel, a wicker chair, a small table, and a view of a marina through a window.

A modern building with a curved facade and a sign that reads "MONSARAZ."

A hotel room with two beds, a view of the city, a dining area, and a large window.

12. The Monsaraz San Diego, Tapestry Collection by Hilton

1.6 km from Shelter Island

Deborah

HK$1,216

HK$1,398 total

includes taxes & fees

12 Nov - 13 Nov

A marina with boats, a yacht, and a balcony with two chairs and a table.

A pool area with lounge chairs and umbrellas, a bar, and a view of boats in the background.

A hotel with a Mediterranean architectural style, featuring a curved entrance, palm trees, and a well-lit driveway.

A large, domed building with a central fountain, surrounded by well-maintained gardens and a calm reflective pool.

13. Kona Kai San Diego

0.3 km from Shelter Island

Michael

HK$1,563

HK$2,268 total

includes taxes & fees

25 Oct - 26 Oct

A balcony with a sofa, chairs, and a small table, overlooking a clear blue sky and palm trees.

A neatly made bed with white linens and multiple pillows, a bedside table with a clock and books, and a wall-mounted lamp.

A bathroom with a marble wall, a toilet, a bathtub, a sink, and a mirror.

A hotel with a sign reading 'LYFE INN SUITES,' a two-story structure with a balcony on the second floor, and a parking lot in front.

14. LYFE INN & SUITES by AGA - San Diego Airport/Point Loma

1.2 km from Shelter Island

Carolina

HK$840

HK$948 total

includes taxes & fees

18 Oct - 19 Oct

An aerial view of a marina with numerous boats docked, surrounded by a residential area with buildings and streets.

A hotel room with two beds, a desk, a chair, a TV, and a window with blinds.

A rooftop patio with wicker furniture and palm trees, overlooking a marina.

A hotel rooftop with a swimming pool, outdoor seating, and a view of the marina and cityscape.

15. Comfort Inn San Diego Airport At The Harbor

1.6 km from Shelter Island

Sean

HK$749

HK$846 total

includes taxes & fees

17 Nov - 18 Nov

A bedroom with a bed, a nightstand, a TV, and a view of the outdoors.

A reception area with a wooden reception desk, a computer, and a chair.

A motel with a covered parking area, a blue car parked in the lot, and a building with blue doors.

A compact kitchen with a refrigerator, microwave, sink, and a small countertop.

16. Hotel Point Loma

1.5 km from Shelter Island

Clint

HK$700

HK$838 total

includes taxes & fees

9 Nov - 10 Nov

A marina with numerous boats docked, a clear sky with the sun setting, and a cityscape in the background.

A hotel room with a large bed, a red armchair, a balcony with a view of boats and buildings, and a lamp on the nightstand.

A modern hotel lobby with a wooden floor, two white armchairs, a reception desk, an ATM, and a staircase.

A hotel room with a large bed, two bedside tables with lamps, a wardrobe, and a bench.

17. Ramada by Wyndham San Diego Airport

1.6 km from Shelter Island

Aaron

HK$848

HK$973 total

includes taxes & fees

1 Nov - 2 Nov

A modern reception area with a wooden bench and a green hedge.

A modern hotel with a prominent 'HOTEL AQUA MAR' sign, large windows, and a visible seating area inside.

A beige upholstered sofa with blue and yellow patterned cushions, positioned in a room with a wooden floor and a green textured wall.

18. Hotel Aqua Mar

1.7 km from Shelter Island

Kathryn

HK$629

HK$709 total

includes taxes & fees

18 Oct - 19 Oct

An outdoor patio area with seating arrangements, a pergola, and a green wall.

A hotel room with a bed, a chair, a small table, a plant, and a door leading to a bathroom.

A two-story building with a colorful facade, a large peace sign above the entrance, and a pink picket fence in front.

A hallway with wooden flooring, a framed artwork of a turtle, and a trash bin.

19. Samesun Ocean Beach - Hostel

Ocean Beach, 4.3 km from Shelter Island

Robert

HK$432

HK$488 total

includes taxes & fees

27 Oct - 28 Oct

A couple walking hand in hand on a sandy beach with the ocean in the background.

A narrow pathway flanked by buildings with large windows and a well-maintained garden.

A cozy living room with a fireplace, a sofa, a dining table, and a chair.

A pathway flanked by lush tropical plants and a building with a large archway.

20. 1906 Lodge

5.9 km from Shelter Island

Judith

HK$2,111

HK$2,326 total

includes taxes & fees

1 Nov - 2 Nov

View all properties

Compare popular hotels close to Shelter Island

Property	Property class	Guest rating
Hampton Inn & Suites San Diego Airport Liberty Station	9.2 Wonderful 1,727 reviews	View
Homewood Suites by Hilton San Diego Airport/Liberty Station	9.4 Exceptional 1,701 reviews	View
Courtyard by Marriott San Diego Airport/Liberty Station	9.2 Wonderful 1,247 reviews	View
Humphreys Half Moon Inn	9.2 Wonderful 3,133 reviews	View
Best Western Plus Island Palms Hotel & Marina	9.0 Wonderful 1,608 reviews	View

Top Shelter Island Hotel Reviews

Bay Club Hotel & Marina

10/10 Excellent

"The hotel was nice and the location is excellent. Friendly staff, easily accessible, and beautiful views. The neds were probably the most comfortable I've very had in a hotel. Will definitely book there again."

The Pearl Hotel

10/10 Excellent

"The room I stayed in was exceptionally comfortable; the AC was reliable, the shower was clean, and the bed was very relaxing - the entire vibe of the hotel is relaxing, especially the bar and pool, which was lively with people during the evening. The staff was kind too and were quick to help with a room key issue. The location is also only a brief drive away from all the major points of interest in the city. I would choose to stay here again during a future San Diego trip."

Courtyard by Marriott San Diego Airport/Liberty Station

8/10 Good

"I recommend the hotel"

DoubleTree by Hilton San Diego Bayside

10/10 Excellent

"They let us check in early and check out late. Shuttling was convenient. The cruise pickup driver was weirdly super stressed but otherwise everything was great. Really liked patios to the pool off of building 3. Great stay and will stay again!"

Homewood Suites by Hilton San Diego Airport/Liberty Station

10/10 Excellent

"I have never been in a hotel where every person working there was as cheerful and helpful and customer oriented. The rooms were excellent. The location by the airport was perfect. I wouldn't hesitate to book again."

Comfort Inn San Diego Airport At The Harbor

10/10 Excellent

"Food along the waterfront is wonderful"

Sea Harbor Hotel

10/10 Excellent

"⭐ 10/10 – Amazing Stay and Wonderful Customer Service! I absolutely loved my stay at Sea Harbor Hotel! I made a very last-minute reservation around 7 PM during Tropical Storm Rachel and arrived about an hour later, completely soaking wet and just praying everything went smoothly with my Expedia booking. Thankfully, check-in was a breeze! The gentleman at the front desk was friendly, welcoming, and even joked around with me a little, which was exactly what I needed after such a stressful evening. He reminded me of my dad. Our room was wonderful! It was incredibly clean, comfortable, and quiet. The location was also fantastic, with so many great places nearby to grab something to eat. What really stood out was how understanding and accommodating the staff were when I experienced a family emergency that required an unexpected, last-minute change to my plans. Their kindness and flexibility meant so much during an already stressful situation. I'm so glad we ended up staying here! Between the hospitality, cleanliness, and convenient location, Sea Harbor Hotel exceeded my expectations. I will absolutely be returning on my next trip to San Diego! 10/10 – Highly recommend!"

The Monsaraz San Diego, Tapestry Collection by Hilton

10/10 Excellent

"Beautiful place, very clean, Staff very nice"

LYFE INN & SUITES by AGA - San Diego Airport/Point Loma

8/10 Good

"The location and the room itself were great! Close to pretty much anything you need. Even a quick mini mart right across the street. Room was comfortable. The only issue I had was seeing a roach the morning of my departure, crawling by the trash can inside the room. For that alone I probably would not stay at this location again. If you need a quick overnight stay though and don’t mind a bug or two, this is the spot."

Other attractions near Shelter Island

Vessel Restaurant

After visiting Vessel Restaurant, make a plan to see the other sights and activities in San Diego. In the area, take in the great live music and beautiful sunsets.

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Kellogs Beach

Why not spend a lazy afternoon at Kellogs Beach during your trip to San Diego? Wander the seaside and beautiful beaches in the area.

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Humphreys Concerts by the Bay

7.4/10 (6 reviews)

You can enjoy a show at Humphreys Concerts by the Bay on your trip to San Diego. Discover the beautiful sunsets and top-notch restaurants in this walkable area.

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Humphreys Backstage Live

Humphreys Backstage Live is just one of the places to see in San Diego, so why not enjoy the other things to explore during your travels? Stroll along the waterfront or discover the area's beautiful sunsets.

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USS Recruit

You can spend time exploring the galleries in USS Recruit during your trip to San Diego. Stroll along the area's marina or experience its great live music.

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Liberty Station Conference Center

Learn about the events happening in Liberty Station Conference Center during your trip to San Diego. Wander the seaside and beautiful beaches in the area.

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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 38 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 Humphreys Half Moon Inn.

How many hotels will I be able to find near Shelter Island?

Expedia has 38 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 Whaley House 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.

San Diego Shelter Island Hotels

Change your mind

Treat yourself

Be picky

Check prices for these dates

Filter by

Star rating

Guest rating

Our top choices for Shelter Island hotels

1. Hampton Inn & Suites San Diego Airport Liberty Station

2. Homewood Suites by Hilton San Diego Airport/Liberty Station

3. Courtyard by Marriott San Diego Airport/Liberty Station

4. Humphreys Half Moon Inn

5. Best Western Plus Island Palms Hotel & Marina

6. Hilton San Diego Airport/Harbor Island

7. TownePlace Suites by Marriott San Diego Airport/Liberty Station

8. The Pearl Hotel

9. DoubleTree by Hilton San Diego Bayside

10. Best Western Yacht Harbor Hotel

11. Sea Harbor Hotel

12. The Monsaraz San Diego, Tapestry Collection by Hilton

13. Kona Kai San Diego

14. LYFE INN & SUITES by AGA - San Diego Airport/Point Loma

15. Comfort Inn San Diego Airport At The Harbor

16. Hotel Point Loma

17. Ramada by Wyndham San Diego Airport

18. Hotel Aqua Mar

19. Samesun Ocean Beach - Hostel

20. 1906 Lodge

Compare popular hotels close to Shelter Island

Top Shelter Island Hotel Reviews

Bay Club Hotel & Marina

The Pearl Hotel

Courtyard by Marriott San Diego Airport/Liberty Station

DoubleTree by Hilton San Diego Bayside

Homewood Suites by Hilton San Diego Airport/Liberty Station

Comfort Inn San Diego Airport At The Harbor

Sea Harbor Hotel

The Monsaraz San Diego, Tapestry Collection by Hilton

LYFE INN & SUITES by AGA - San Diego Airport/Point Loma

Other attractions near Shelter Island

Vessel Restaurant

Kellogs Beach

Humphreys Concerts by the Bay

Humphreys Backstage Live

USS Recruit

Liberty Station Conference Center

Frequently asked questions

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