4 Best Shelter Island San Diego Hotels

Shelter Island sometimes feels like one of San Diego’s secret hideaways. Built in the 1950s, this manmade peninsula is connected to the Point Loma community on the mainland. It serves as a literal shelter for boats docked in the harbor.

One street, Shelter Island Drive, runs across the 1.3-mile-long island, home to (in a nutshell) four hotels, public art along a nice walking trail, Bali Hai restaurant, and a yacht club.

Shelter Island’s proximity to the airport and reasonable hotel pricing make it appealing for a San Diego vacation base. You may also stay here in advance of fishing trips that depart from here or need a break from your yacht (this is one of the only places with water deep enough to park them).

There are four Shelter Island San Diego hotels on the peninsula ranging in price from moderate to budget. Plus, they have water views galore. You could also stay in one of the hotels near Shelter Island in the Point Loma area, where you might have more dining options within walking distance.

All four island hotels are below. If you are set on being right by the terminal instead, see my guide to the best hotels near the San Diego airport.

Shelter Island itself is a short list, just these four hotels on the water. For the boutique, bayfront, and Liberty Station options that surround it, see my full guide to Point Loma hotels.

We independently select featured hotels and may earn a commission if you book through the links below.

1. Kona Kai Resort & Spa

1551 Shelter Island Drive, San Diego, CA 92106

Best for: the most resort-like stay on the island, with a full spa and complimentary cruiser bikes around the grounds.

What to Expect: Kona Kai Resort & Spa offers a collection of recently renovated island-inspired guest rooms and suites with a SoCal twist. Surrounded by eleven acres of lush tropical gardens, the hotel provides complimentary cruiser bikes to tour around the property.

Newly expanded and transformed, it’s an island paradise overlooking the majestic San Diego Bay. Your kids will especially love the nightly bonfires and S’mores Kits for purchase. It is the most luxurious option on Shelter Island.

Resort Amenities:

• SpaTerre, luxurious personalized treatments and services
• Tiki Bar & Pool – family-friendly pool with food and drink service
• Paloma Pool & Paloma Pool Bar and cabanas with food and drink service
• Pool cabana rentals include TV, Wi-Fi, comfortable seating, water, and snacks
• Indoor/outdoor high-end fitness center with waterfront views
• Vessel Restaurant + Bar, serving innovative SoCal-inspired cuisine
• Island Boutique, selling stylish clothing, tumblers, high-end products, and essentials

Good to Know: Pet-friendly resort, accessible rooms, connecting rooms available, daily resort amenities fee of $48 (subject to change – check before you book), Tesla charging stations, 15% military discount at SpaTerre, AAA, senior, and government rates, must be 16+ to use fitness facilities, non-smoking hotel, pets not allowed in pools or on private bay beach (no swimming), paid daily parking.

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2. Humphreys Half Moon Inn

2303 Shelter Island Drive, San Diego, CA 92106

Best for: travelers who want live music at the door, since the hotel hosts Humphreys Concerts by the Bay through the summer.

What to Expect: One of the few Shelter Island San Diego hotels, Humphreys Half Moon Inn is situated on San Diego Bay. Reminiscent of a contemporary tropical retreat, guestrooms, and deluxe suites feature tasteful island-style décor, including custom headboards.

Each accommodation provides a patio or balcony offering bay, marina, or pool views. Several fun recreational opportunities are available, including the waterfront walking/jogging path adjacent to the hotel.

Amenities:

• Spacious and well-appointed guestrooms and suites
• Humphreys Concerts by the Bay
• Backstage LIVE Music Club
• Tropical-inspired heated outdoor swimming pool with whirlpool spa
• Conference facilities, event space, meeting space, and banquet room
• Outdoor waterfront special event area and garden wedding ceremony site
• Humphreys Half Moon Inn Marina – private marina
• Seasonal poolside bar
• Fitness center
• Massage facility and in-room massages
• Customized trip planning provided by the front desk staff
• One-hour complimentary bicycle rentals
• Grand Marina Suites, and Marina and Garden View Suites have fully-equipped kitchens
• A limited number of connecting rooms at Humphreys Half Moon Inn
• Short drive to SeaWorld San Diego and Balboa Park

Good to Know: Non-smoking hotel, guest laundry facilities, dry cleaning service, ADA accessible rooms, guest parking $25 per night, ATM, multilingual staff, mandatory Half Moon Pass fee $20 a night, 48-hour cancellation policy, kids 17 and under stay free with accompanying adult, no pets.

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3. Best Western Plus Island Palms Hotel & Marina

2051 Shelter Island Drive, San Diego, CA 92106

Best for: boaters and families who want a big marina and two pools, at a Best Western price.

What to Expect: This isn’t your average Best Western — it feels more resort-like. Boasting a retro San Diego style, Best Western Plus Island Palms Hotel is one of the only hotels on Shelter Island. Well-appointed guestrooms and suites feature San Diego Bay, a private marina, or downtown views.

This incredible seaside location is ideal for families who want to spend their days exploring. The hotel offers bike rentals and a variety of sailing and boat trips.

Amenities:

• Two outdoor heated pools and a hot tub
• Seasonal poolside food and beverage service
• Blue Wave Bar & Grill, restaurant, cocktail lounge, and table service bar
• Private marina filled with sailboats, cruisers, and super yachts
• Boat slips (6-60 meters) feature hookups for electric, phone, cable, and water
• Two tennis courts
• Waterfront walking trails
• Conference, banquet, and ballroom facilities overlooking Point Loma and the Marina
• Business center, mail services, postal deliveries
• A modest fitness center with treadmills, ellipticals, stationary bikes, and weight equipment
• On-site massage service available through the front desk

Good to Know: Car rental desk, non-smoking hotel, 24-hour front desk, $25 unassigned parking, maximum one car per room, no truck parking, no pets, children 17 and under stay free accompanied by an adult, you’ll be pre-charged on arrival for the full amount of your stay, taxes, plus an additional $50 per night for incidentals, laundry, and dry cleaning service.

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4. The Bay Club Hotel & Marina

2131 Shelter Island Drive, San Diego, CA 92106

Best for: the simplest, best-value stay on the island, with a bayfront happy hour and kids 12 and under free.

What to Expect: Offering a selection of well-appointed nautical-inspired guest rooms and suites, you can relax in style. Chic and spacious accommodations include a patio or a balcony, highlighted by fantastic views.

One of the only hotels on Shelter Island, you’re uniquely positioned near many family-friendly attractions and local excursions. This includes bike rentals, sportfishing, Balboa Park, SeaWorld San Diego, USS Midway Museum, and Old Town San Diego.

Amenities:

• Full-service “green” Bay Club Hotel Marina (boat slips range in size from 3 meters to 25 meters)
• Heated outdoor pool and hot tub
• Fitness center overlooking the Bay Club Hotel Marina
• Free complimentary morning coffee in the lobby
• Bay Club Bar & Grill – California-American style cuisine
• Happy hour daily from 2-6 p.m. (appetizer and drink specials available)
• 2,255 square feet of meeting and event space, including three water-view meeting rooms
• Outdoor seating areas with firepits and outdoor grills
• Luggage storage for guests who arrive earlier than their room reservation
• Hosts small weddings of up to 100 guests

Good to Know: Free Wi-Fi, ADA accessible rooms available, 24-hour notice cancellation policy, kids 12 and under stay free, rollaway beds and cribs $10 a day extra charge, connected rooms available, smoking allowed in select areas, coin laundry available, self-parking $22 a night, only service animals are allowed at the hotel.

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