Top 10 Harbor Island Hotels of 2026

A harbor with multiple sailboats and a bridge in the background.

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Our top choices for Harbor Island hotels

An outdoor terrace with tables and chairs, string lights, and a view of the marina.

1. Hilton San Diego Airport/Harbor Island

Harbor Island

Katherine Martinez

includes taxes & fees

31 Aug - 1 Sept

A balcony with wicker furniture overlooking a marina and a coastal cityscape.

2. Sheraton San Diego Resort

Harbor Island

Morne De

includes taxes & fees

2 Sept - 3 Sept

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

3. Hampton Inn & Suites San Diego Airport Liberty Station

0.7 km from Harbor Island

Ivan

includes taxes & fees

30 Aug - 31 Aug

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

4. DoubleTree by Hilton San Diego Bayside

1.6 km from Harbor Island

Jorge

includes taxes & fees

30 Aug - 31 Aug

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

5. Best Western Yacht Harbor Hotel

1.7 km from Harbor Island

Donald

includes taxes & fees

24 Aug - 25 Aug

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

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

1 km from Harbor Island

Sergio

includes taxes & fees

31 Aug - 1 Sept

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

7. Comfort Inn San Diego Airport At The Harbor

2 km from Harbor Island

Daniel

includes taxes & fees

21 Sept - 22 Sept

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

8. Best Western Plus Island Palms Hotel & Marina

2.3 km from Harbor Island

Jay

includes taxes & fees

7 Sept - 8 Sept

A balcony with a table set for two, overlooking a marina with numerous boats.

9. Bay Club Hotel & Marina

2 km from Harbor Island

Smarika

includes taxes & fees

30 Aug - 31 Aug

A reception area with a stone archway, a reception desk, and potted plants.

10. Holiday Inn Express San Diego Airport - Old Town by IHG

2.9 km from Harbor Island

Tirthankar

includes taxes & fees

30 Aug - 31 Aug

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

11. Humphreys Half Moon Inn

1.8 km from Harbor Island

Michelle

includes taxes & fees

30 Aug - 31 Aug

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

12. Sea Harbor Hotel

2.1 km from Harbor Island

Taylor

includes taxes & fees

24 Aug - 25 Aug

A modern dining area with multiple tables and chairs, large windows, and artwork on the walls.

13. Comfort Inn San Diego Old Town

Old Town San Diego, 2.9 km from Harbor Island

Heather

includes taxes & fees

1 Sept - 2 Sept

A modern hotel lobby with a central seating area, a bar, and a large window providing natural light.

14. Wyndham Garden San Diego Near SeaWorld

3.3 km from Harbor Island

marissa

includes taxes & fees

1 Sept - 2 Sept

A hotel with a central courtyard, palm trees, and a fountain.

15. Hilton Garden Inn San Diego Old Town/SeaWorld Area

Old Town San Diego, 3.7 km from Harbor Island

Cari

includes taxes & fees

20 Sept - 21 Sept

A historic building with a central courtyard and a reflective water feature.

16. Old Town Western Inn & Suites

Old Town San Diego, 2.9 km from Harbor Island

Sayeeda

includes taxes & fees

8 Sept - 9 Sept

A building with a "Bienvenidos" sign, palm trees, and a well-maintained garden.

17. Old Town Inn

3 km from Harbor Island

Layne

includes taxes & fees

1 Sept - 2 Sept

A pool area with lounge chairs and palm trees.

18. Best Western Plus Hacienda Hotel Old Town

Old Town San Diego, 3.3 km from Harbor Island

Robert

includes taxes & fees

30 Aug - 31 Aug

A hotel courtyard with outdoor seating, palm trees, and a view of the ocean at dusk.

19. Wyndham San Diego Bayside

3.3 km from Harbor Island

Jennifer

includes taxes & fees

26 Aug - 27 Aug

20. Hampton Inn San Diego-Downtown

3.3 km from Harbor Island

Velma

includes taxes & fees

6 Sept - 7 Sept

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Where to stay in Harbor Island

Find the best Harbor Island areas for the activities you enjoy most.

A plaza with a traditional building, benches, and a large tree.

Downtown San Diego

Known for its fantastic nightlife, fascinating museums and beautiful waterfront views, there's plenty to explore in Downtown San Diego. Top attractions like Petco Park and Port of San Diego are major draws. Catch the metro at Civic Center Station or Civic Center Station to see more of the city.

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A beach with surfers and swimmers during sunset.

Pacific Beach

Relax in beachside cafés in the morning, surf clean breaks in the afternoon and dance with a youthful club crowd at night at this coastal San Diego strip.

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A roller coaster under construction with scaffolding and a ticket booth in the foreground.

Mission Beach

If you're spending some time in Mission Beach, Mission Beach and Mission Bay are top sights worth seeing.

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Gaslamp Quarter

The historic heart of San Diego has a fascinating history, and today is a thriving hub for food, retail and entertainment.

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An aerial view of a coastal city with a marina, a large body of water, and a peninsula with buildings.

Mission Bay

If you're spending some time in Mission Bay, Mission Bay and Mission and Pacific Beaches are top sights worth seeing.

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Top Harbor Island Hotel Reviews

California Suites Hotel

10/10 Excellent

"Great place to stay"

Courtyard by Marriott San Diego Downtown Little Italy

8/10 Good

"Rooms were updated and clean. Check in and check out was easy. Read several reviews about the terrible parking garage so we opted to park across the street and saved $50 vs paying for the garage. Only tiny issue was they said our room would be cleaned on the 2nd night and we came back and it was not cleaned. Not a huge issue, just had to go down and get clean towels. Location is great! Quiet and right next to the Little Italy Saturday market. We would definitely stay again!"

The Dana on Mission Bay

8/10 Good

"My wife was denied a popsicle on popsicle day! For the rates they charge, a popsicle seems like something everyone should get. The restaurant on site was slightly above average food wise but the service and drinks were excellent. The location, service, views, and gardens were all excellent. As walkers, we both loved the walk along the coast around the marina. Definitely catch the seafood restaurant across the street from the hotel called Sportsman’s Catch (or something similar) amazing fresh fish sandwiches and excellent prices. We saw them loading in fresh caught fish in the back. Over all a 8.5/10…definitely would stay again."

Frequently asked questions

What's it like in Harbor Island?

Harbor Island is a scenic neighbourhood known for its beautiful island views and array of dining options. Consider a visit to San Diego Bay as part of your Harbor Island travel plans.

Where is the best place to stay in Harbor Island?

Based on our traveller data, Sheraton San Diego Resort is one of the top choices for your stay in Harbor Island. This hotel is a short 1-minute walk from San Diego Bay, and it offers a marina and 3 outdoor pools.

How many hotels should I expect to find in the Harbor Island area?

Book one of Expedia's 6 hotels and other accommodation options in Harbor Island and start exploring everything San Diego has to offer.

If I need to cancel my hotel reservation in Harbor Island, will I receive a refund?

Yes, the majority of hotel 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 have a reservation that's non-refundable, you may still be able to cancel and get a refund within 24 hours of your booking. Enter dates in and click on "Search", then you can use the "fully refundable" filter to view the top deals on offer in Harbor Island.

What is there to do around this San Diego neighbourhood?

San Diego Bay is an attraction you might want to check out while you're in Harbor Island. While you're out sightseeing in San Diego, make sure that you visit other sights such as Marine Corps Recruit Depot or Port of San Diego.

Hotels in Harbor Island

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Our top choices for Harbor Island hotels

1. Hilton San Diego Airport/Harbor Island

2. Sheraton San Diego Resort

3. Hampton Inn & Suites San Diego Airport Liberty Station

4. DoubleTree by Hilton San Diego Bayside

5. Best Western Yacht Harbor Hotel

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

7. Comfort Inn San Diego Airport At The Harbor

8. Best Western Plus Island Palms Hotel & Marina

9. Bay Club Hotel & Marina

10. Holiday Inn Express San Diego Airport - Old Town by IHG

11. Humphreys Half Moon Inn

12. Sea Harbor Hotel

13. Comfort Inn San Diego Old Town

14. Wyndham Garden San Diego Near SeaWorld

15. Hilton Garden Inn San Diego Old Town/SeaWorld Area

16. Old Town Western Inn & Suites

17. Old Town Inn

18. Best Western Plus Hacienda Hotel Old Town

19. Wyndham San Diego Bayside

20. Hampton Inn San Diego-Downtown

Where to stay in Harbor Island

Downtown San Diego

Pacific Beach

Mission Beach

Gaslamp Quarter

Mission Bay

Top Harbor Island Hotel Reviews

California Suites Hotel

Frequently asked questions