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

Hotels in Harbor Island, San Diego

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Check prices for these dates

This weekend
16 Oct - 18 Oct
Next weekend
23 Oct - 25 Oct

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Our top choices for Harbor Island hotels

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

1. Hilton San Diego Airport/Harbor Island

Hilton San Diego Airport/Harbor Island
3.5 star property
Harbor Island
8.8 out of 10, Excellent, (1,208 reviews)
"Excellent place to stay"
United States
Amos
The price is RM666
RM766 total
includes taxes & fees
8 Nov - 9 Nov
Hilton San Diego Airport/Harbor Island
A balcony with wicker furniture overlooking a marina and a coastal cityscape.

2. Sheraton San Diego Resort

Sheraton San Diego Resort
4.0 star property
Harbor Island
8.6 out of 10, Excellent, (3,758 reviews)
"Great place to stay"
United States
andrew
The price is RM568
RM859 total
includes taxes & fees
25 Oct - 26 Oct
Sheraton San Diego Resort
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

Hampton Inn & Suites San Diego Airport Liberty Station
2.5 star property
0.7 km from Harbor Island
9.2 out of 10, Wonderful, (1,731 reviews)
"Love to stay here, very nice accommodations, quiet, great service, the airport shuttle very convenient."
United States
MANUEL
The price is RM666
RM766 total
includes taxes & fees
9 Nov - 10 Nov
Hampton Inn & Suites San Diego Airport Liberty Station
A spacious lounge area with a high ceiling, a fireplace, and large windows offering a view of the outdoors.

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

TownePlace Suites by Marriott San Diego Airport/Liberty Station
3.0 star property
0.7 km from Harbor Island
8.8 out of 10, Excellent, (1,007 reviews)
"Such a great place to stay"
United States
Chase
The price is RM718
RM825 total
includes taxes & fees
8 Nov - 9 Nov
TownePlace Suites by Marriott San Diego Airport/Liberty Station
A hotel complex with multiple buildings, a landscaped garden, and a body of water reflecting the sunset.

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

Homewood Suites by Hilton San Diego Airport/Liberty Station
3.0 star property
1 km from Harbor Island
9.4 out of 10, Exceptional, (1,708 reviews)
"Amazing place location and hotel staff were amazing."
United States
Orlyn
The price is RM747
RM858 total
includes taxes & fees
27 Oct - 28 Oct
Homewood Suites by Hilton San Diego Airport/Liberty Station
A hotel room with two beds, a desk, a chair, and a large window with a view of the outdoors.

6. Best Western Yacht Harbor Hotel

Best Western Yacht Harbor Hotel
2.5 star property
1.8 km from Harbor Island
8.4 out of 10, Very good, (2,096 reviews)
"nice stay"
United States
Falizity
The price is RM466
RM534 total
includes taxes & fees
8 Nov - 9 Nov
Best Western Yacht Harbor Hotel
A modern hotel room with a large bed, bedside tables, a desk, and a wardrobe.

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

Holiday Inn Express San Diego Airport - Old Town by IHG
2.5 star property
2.9 km from Harbor Island
9.2 out of 10, Wonderful, (1,088 reviews)
"Love the hotel, the breakfast was good and the staff was exceptional."
United States
Patricia
The price is RM625
RM718 total
includes taxes & fees
25 Oct - 26 Oct
Holiday Inn Express San Diego Airport - Old Town by IHG
A hotel courtyard with outdoor seating, palm trees, and a view of the ocean at dusk.

8. Wyndham San Diego Bayside

Wyndham San Diego Bayside
4.0 star property
3.3 km from Harbor Island
8.4 out of 10, Very good, (6,326 reviews)
"Wonderful staff and a great location"
United States
Jonathan
The price is RM621
RM863 total
includes taxes & fees
25 Oct - 26 Oct
Wyndham San Diego Bayside
A modern building with a sloped roof and large windows, surrounded by palm trees and a well-maintained garden.

9. Best Western Plus Island Palms Hotel & Marina

Best Western Plus Island Palms Hotel & Marina
3.0 star property
2.3 km from Harbor Island
9.0 out of 10, Wonderful, (1,618 reviews)
"This hotel is amazing. This was our 2nd time staying there and we will be back."
United States
Sarah
The price is RM569
RM654 total
includes taxes & fees
9 Nov - 10 Nov
Best Western Plus Island Palms Hotel & Marina
A hotel room with a large window offering a city view, a bed, a chair, and a small table.

10. The DEXTRO Little Italy, BW Premier Collection

The DEXTRO Little Italy, BW Premier Collection
3.0 star property
4 km from Harbor Island
8.8 out of 10, Excellent, (2,275 reviews)
"Clean room, great staff and a really good breakfast"
United States
Abeer
The price is RM621
RM720 total
includes taxes & fees
5 Nov - 6 Nov
The DEXTRO Little Italy, BW Premier Collection
A resort with two-story buildings, balconies, and a pool area.

11. Humphreys Half Moon Inn

Humphreys Half Moon Inn
3.5 star property
1.8 km from Harbor Island
9.2 out of 10, Wonderful, (3,138 reviews)
"We had a great stay!"
United States
Svenja
The price is RM772
RM969 total
includes taxes & fees
9 Nov - 10 Nov
Humphreys Half Moon Inn
A buffet area with a checkered floor, a variety of food items, and a coffee station.

12. Hampton Inn San Diego-Downtown

Hampton Inn San Diego-Downtown
2.5 star property
3.4 km from Harbor Island
8.2 out of 10, Very good, (2,797 reviews)
"Clean rooms, great breakfast"
United States
debbie
The price is RM599
RM695 total
includes taxes & fees
25 Oct - 26 Oct
Hampton Inn San Diego-Downtown
A balcony with a table set for two, overlooking a marina with numerous boats.

13. Bay Club Hotel & Marina

Bay Club Hotel & Marina
3.5 star property
2 km from Harbor Island
9.2 out of 10, Wonderful, (4,010 reviews)
"Great location and friendly staff."
United States
Thuan
The price is RM625
RM718 total
includes taxes & fees
26 Oct - 27 Oct
Bay Club Hotel & Marina
A hotel with a central courtyard, palm trees, and a fountain.

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

Hilton Garden Inn San Diego Old Town/SeaWorld Area
3.0 star property
Old Town San Diego, 3.8 km from Harbor Island
8.8 out of 10, Excellent, (1,533 reviews)
"Nice, clean hotel for a quick stay."
United States
Kristen
The price is RM517
RM595 total
includes taxes & fees
9 Nov - 10 Nov
Hilton Garden Inn San Diego Old Town/SeaWorld Area
A hotel breakfast area with a long counter displaying various food items, including fruits, pastries, and a coffee station.

15. Best Western Inn & Suites San Diego – Zoo/SeaWorld Area

Best Western Inn & Suites San Diego – Zoo/SeaWorld Area
2.5 star property
4.3 km from Harbor Island
8.0 out of 10, Very good, (3,074 reviews)
"Clean and spacious room, good breakfast, nice staff."
United States
Antonia
The price is RM560
RM644 total
includes taxes & fees
20 Oct - 21 Oct
Best Western Inn & Suites San Diego – Zoo/SeaWorld Area
A modern building with multiple windows, outdoor seating, and a chessboard.

16. Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town

Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town
4.0 star property
3.4 km from Harbor Island
9.2 out of 10, Wonderful, (1,414 reviews)
"Clean, convenient and the beds were super comfy!"
United States
Tammy
The price is RM691
RM794 total
includes taxes & fees
27 Oct - 28 Oct
Hampton Inn & Suites by Hilton San Diego SeaWorld Near Old Town
A modern dining area with multiple tables and chairs, large windows, and artwork on the walls.

17. Comfort Inn San Diego Old Town

Comfort Inn San Diego Old Town
2.5 star property
Old Town San Diego, 2.9 km from Harbor Island
8.2 out of 10, Very good, (2,077 reviews)
"Location was good since we were going to the marines base restaurants we’re walking distance and the breakfast fast good."
United States
Paula
The price is RM449
RM516 total
includes taxes & fees
27 Oct - 28 Oct
Comfort Inn San Diego Old Town
An outdoor seating area with a fire feature, surrounded by palm trees and modern buildings.

18. Homewood Suites by Hilton San Diego Hotel Circle/SeaWorld Area

Homewood Suites by Hilton San Diego Hotel Circle/SeaWorld Area
3.0 star property
4.3 km from Harbor Island
8.8 out of 10, Excellent, (1,737 reviews)
"Clean room, very friendly staff, great breakfast."
United States
Edith
The price is RM566
RM650 total
includes taxes & fees
8 Nov - 9 Nov
Homewood Suites by Hilton San Diego Hotel Circle/SeaWorld Area
A pool area with lounge chairs and palm trees.

19. Best Western Plus Hacienda Hotel Old Town

Best Western Plus Hacienda Hotel Old Town
3.0 star property
Old Town San Diego, 3.3 km from Harbor Island
8.4 out of 10, Very good, (2,179 reviews)
"Wonderful place to stay"
United States
shon
The price is RM584
RM672 total
includes taxes & fees
27 Oct - 28 Oct
Best Western Plus Hacienda Hotel Old Town
A modern hotel lobby with a central seating area, a bar, and a large window providing natural light.

20. Wyndham Garden San Diego Near SeaWorld

Wyndham Garden San Diego Near SeaWorld
3.0 star property
3.3 km from Harbor Island
7.4 out of 10, Good, (4,206 reviews)
"Nice place"
United States
Virginia
The price is RM428
RM492 total
includes taxes & fees
20 Oct - 21 Oct
Wyndham Garden San Diego Near SeaWorld
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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Where to stay in Harbor Island

Find the best Harbor Island areas for the activities you enjoy most.
A large stadium with the sign "Cobo Park" and palm trees around it.

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.

A pier extending into the ocean with buildings at the end, under a partly cloudy sky.

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.

A theater marquee with ornate designs and the name "Gaslamp Quarter".

Gaslamp Quarter

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

A coastal cityscape with a long sandy beach, a pier, and dense urban buildings.

Mission Beach

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

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 Ski Beach are top sights worth seeing.

Top Harbor Island Hotel Reviews

Wyndham San Diego Bayside

Wyndham San Diego Bayside

10/10 Excellent
"Older hotel but honestly the location and staff made up for it!"
Amanda 2-night trip
Posted 3 hours ago
Wyndham San Diego Bayside

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.