The Best Hotels in Harbor Island, San Diego - 2026 Updated Prices

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

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Our top choices for Harbor Island hotels

1. Hilton San Diego Airport/Harbor Island

Harbor Island

Amos

Rp3.307.186 total

includes taxes & fees

20 Sept - 21 Sept

Studio Suite, 1 King Bed with Sofa bed, Balcony | View from room

2. Sheraton San Diego Resort

Harbor Island

Kathleen

Rp4.318.925 total

includes taxes & fees

27 Sept - 28 Sept

3. Hampton Inn & Suites San Diego Airport Liberty Station

0.7 km from Harbor Island

David

Rp3.569.240 total

includes taxes & fees

5 Oct - 6 Oct

4. Humphreys Half Moon Inn

1.8 km from Harbor Island

Laura

Rp4.183.192 total

includes taxes & fees

5 Oct - 6 Oct

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

1 km from Harbor Island

Orlyn

Rp4.038.423 total

includes taxes & fees

28 Sept - 29 Sept

6. Bay Club Hotel & Marina

2 km from Harbor Island

Jennifer

Rp3.284.760 total

includes taxes & fees

10 Sept - 11 Sept

Premium bedding, in-room safe, desk, laptop workspace

7. Best Western Plus Marina Gateway Hotel

11.6 km from Harbor Island

Alexander

Rp2.700.693 total

includes taxes & fees

10 Sept - 11 Sept

8. Sea Harbor Hotel

2.1 km from Harbor Island

Jorge

Rp2.277.661 total

includes taxes & fees

10 Sept - 11 Sept

9. Fairfield Inn & Suites San Diego Old Town

Old Town San Diego, 3 km from Harbor Island

David

Rp3.014.124 total

includes taxes & fees

27 Sept - 28 Sept

10. Comfort Inn San Diego Old Town

Old Town San Diego, 2.9 km from Harbor Island

Heather

Rp2.464.584 total

includes taxes & fees

30 Sept - 1 Oct

11. Residence Inn by Marriott San Diego Downtown/Gaslamp Quarter

Gaslamp Quarter, 4.8 km from Harbor Island

RheaAnn

Rp2.800.690 total

includes taxes & fees

13 Sept - 14 Sept

12. Courtyard by Marriott Old Town

Old Town San Diego, 3 km from Harbor Island

Paola

Rp3.085.038 total

includes taxes & fees

28 Sept - 29 Sept

Studio Suite, 1 King Bed, Courtyard View | View from room

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

3.4 km from Harbor Island

Joshua

Rp3.140.994 total

includes taxes & fees

27 Sept - 28 Sept

14. Wyndham Garden San Diego Near SeaWorld

3.3 km from Harbor Island

Nayla

Rp1.944.020 total

includes taxes & fees

15 Sept - 16 Sept

15. Old Town Inn

3 km from Harbor Island

Layne

Rp3.020.674 total

includes taxes & fees

14 Sept - 15 Sept

3 restaurants; breakfast, lunch and dinner served

16. Wyndham San Diego Bayside

3.3 km from Harbor Island

Jennifer

Rp3.725.751 total

includes taxes & fees

20 Sept - 21 Sept

Standard Room, 1 King Bed, Non Smoking, Bay View | Premium bedding, pillow-top beds, in-room safe, desk

17. The DEXTRO Little Italy, BW Premier Collection

4 km from Harbor Island

Bradley

Rp3.284.236 total

includes taxes & fees

23 Sept - 24 Sept

Room, 2 Queen Beds (Trendy, Firepit) | Lobby

18. Town and Country San Diego

5.5 km from Harbor Island

Sol

Rp4.970.188 total

includes taxes & fees

10 Sept - 11 Sept

Suite, 1 King Bed | In-room safe, desk, blackout curtains, iron/ironing board

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

2.9 km from Harbor Island

Faleoalii Iereneo

Rp2.857.661 total

includes taxes & fees

23 Sept - 24 Sept

20. Comfort Inn Sea World Area

3.3 km from Harbor Island

Rick

Rp2.325.650 total

includes taxes & fees

29 Sept - 30 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 pier at sunset with people sitting and standing, waves crashing below.

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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Gaslamp Quarter

San Diego’s historic heart has shed its seedy past to emerge as one of the city’s premier dining, shopping and entertainment hubs.

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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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A beach with palm trees, a hotel, and people enjoying the sand and water.

Ocean Beach

Ocean Beach is beloved for its stunning beaches. Take some time to explore sights in the area like Ocean Beach and Dog Beach.

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Top Harbor Island Hotel Reviews

Omni San Diego Hotel at the Ballpark

8/10 Good

"Excellent staff!! Access to ballpark rocked!! Need to update rooms bathroom!! Thx u!! Will be back!!!"

The Sofia Hotel

10/10 Excellent

"We had a wonderful stay at The Sofia Hotel! The hotel has so much charm and character, and the location was incredibly convenient for everything we wanted to do in San Diego. One thing that really stood out to us was the housekeeping. Our room was refreshed and tidied up every single day, which is something you just don’t find very often anymore! It was such a nice feeling coming back after a long day to a clean, refreshed room and a neatly made bed. Those little touches really made our stay feel special. The staff was friendly and helpful throughout our stay, and overall we had a great experience. We would absolutely stay at The Sofia again on another trip to San Diego!"

Hard Rock Hotel San Diego

10/10 Excellent

"It’s a fun well located super clean hotel with great entertainment and proximity to the fun gas lamp and Padres field. Pool is small a somewhat lame - but expected for a rooftop. Our coffee machine was malfunctioning but again… we could have asked for a replacement and that’s on us."

Paradise Point Resort & Spa

8/10 Good

"This hotel is very central and a good base. The room was clean and a good size. Moving around the property is a good way to make your step mark. Dining options are limited to 2 restaurants on premises and a market. Will recommend to bring your own snacks and water if you have a large group. Has a marina in place and you have multiple rental options. The views of the cove are great"

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.

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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. Humphreys Half Moon Inn

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

6. Bay Club Hotel & Marina

7. Best Western Plus Marina Gateway Hotel

8. Sea Harbor Hotel

9. Fairfield Inn & Suites San Diego Old Town

10. Comfort Inn San Diego Old Town

11. Residence Inn by Marriott San Diego Downtown/Gaslamp Quarter

12. Courtyard by Marriott Old Town

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

14. Wyndham Garden San Diego Near SeaWorld

15. Old Town Inn

16. Wyndham San Diego Bayside

17. The DEXTRO Little Italy, BW Premier Collection

18. Town and Country San Diego

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

20. Comfort Inn Sea World Area

Where to stay in Harbor Island

Downtown San Diego

Pacific Beach

Gaslamp Quarter

Mission Beach

Ocean Beach

Top Harbor Island Hotel Reviews

Omni San Diego Hotel at the Ballpark

Frequently asked questions