Prime Shelter Island Hotels in San Diego's Coastal Gem

We checked thousands of reviews on and to find the best hotels for your stay
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Agostina Lombardi

Updated: 29 October 2024 · 2 min

San Diego, a vibrant coastal city in Southern California, is a paradise for beach lovers and culture enthusiasts alike. Nestled in the very heart of this beautiful city lies Shelter Island, a picturesque enclave known for its stunning waterfront views and array of luxury accommodations. When it comes to finding the perfect place to stay in San Diego, the hotels on Shelter Island offer a unique blend of relaxation and sophistication, making them an ideal choice for travelers seeking a peaceful retreat by the sea.

With its palm-lined streets, marina-inspired architecture, and panoramic vistas of the bay, Shelter Island exudes a sense of tranquility that sets it apart from other parts of the city. From boutique hotels with personalized service to upscale resorts with top-notch amenities, the accommodations on this island cater to every style and preference. Whether you're looking for a romantic getaway, a family-friendly escape, or a business trip with a touch of leisure, Shelter Island has something for everyone.

Indulge in waterfront dining, soak up the sunshine on sandy beaches, or embark on a sailing adventure right from your hotel's doorstep - the possibilities for relaxation and exploration are endless on Shelter Island. By immersing yourself in the laid-back charm and coastal beauty of this hidden gem in San Diego, you'll discover a retreat like no other, where luxury meets serenity and every moment is a chance to create unforgettable memories.
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Our Top 3

(Sorted by rating & number of reviews)

1. Kona Kai Resort & Spa, A Noble House Resort
2. Humphreys Half Moon Inn
3. Best Western Plus Island Palms Hotel & Marina

Hotels on Shelter Island San Diego

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San Diego
Mar 17, 2026 - Mar 18, 2026

Kona Kai Resort & Spa, A Noble House Resort

7.3

Good

(33 Reviews)

+ 282 photos
Kona Kai Resort & Spa is a haven of tranquility and luxury, nestled on the secluded tip of Shelter Island. Boasting a private beach, marina, and stunning views of the bay, this resort embodies the essence of coastal elegance in San Diego. With spacious rooms and suites, a full-service spa, waterside dining options, and a range of activities including water sports and yacht charters, Kona Kai offers a complete retreat for guests seeking a pampering escape on Shelter Island.
Address: 1551 Shelter Island Drive
Rating: Good 7.3 (33 Reviews)
Rooms: 170
Price: From 133$

Hotels on Shelter Island San Diego

Humphreys Half Moon Inn

8.6

Good

(1199 Reviews)

+ 211 photos
Humphreys Half Moon Inn, a tropical oasis on Shelter Island, exudes a laid-back charm with its lush gardens, outdoor pool, and live entertainment venue. Featuring spacious rooms with balconies or patios overlooking the marina, this hotel offers a serene respite from the hustle and bustle of the city. Guests can enjoy on-site dining, bike rentals, paddleboard yoga sessions, and easy access to Shelter Island's attractions, making Humphreys Half Moon Inn a popular choice for those seeking a relaxed yet upscale stay in San Diego.
Address: 2303 Shelter Island Drive
Rating: Good 8.6 (1199 Reviews)
Rooms: 182
Price: From 148$

Best Western Plus Island Palms Hotel & Marina

8.3

Good

(1141 Reviews)

+ 301 photos
Best Western Plus Island Palms Hotel & Marina is a charming waterfront retreat featuring comfortable accommodations and panoramic bay views. With two heated pools, a waterfront bar and grill, and a marina with access to water activities, this hotel provides an ideal setting for a relaxing stay on Shelter Island. Whether guests choose a room with a private patio or a suite with a fully equipped kitchen, the hotel's warm hospitality and convenient amenities make it a popular choice for travelers seeking a home away from home in San Diego.
Address: 2051 Shelter Island Drive
Rating: Good 8.3 (1141 Reviews)
Rooms: 227
Price: From 100$