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.

We break down both options below.

Note from Katie: We independently choose all featured hotels. Booking methods mentioned are popular with our readers or ones we think offer the best value. If you book through select links, we may earn a commission and appreciate you supporting our business. Prices and amenities are subject to change. Our editorial guidelines.

1. Kona Kai Resort & Spa

Kona Kai has one of the best hotel pools in San Diego.

Address: 1551 Shelter Island Drive, San Diego, CA 92106

Category: Moderate

Location: On Shelter Island

Notable Features: San Diego Bay views and Private Beach

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 on the private beach 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 $42 (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

A kitchen in a room at Humphrey's Half Moon Bay Inn on Shelter Island San Diego.

Address: 2303 Shelter Island Drive, San Diego, CA 92106

Category: Moderate

Location: On Shelter Island

Notable Features: Award-winning Humphreys So Cal Dining and Music and private marina

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 $20 per night, ATM, multilingual staff, mandatory Humphreys Half Moon Inn Pass fee $17 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

Best Western Plus Island Palms Hotel & Marina

Address: 2051 Shelter Island Drive, San Diego, CA, 92106

Category: Moderate

Location: On Shelter Island

Notable Features: Island Palms Hotel Marina with 188 berths and waterfront walking trail 

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
  • Pure Body Spa is located in the Del Mar Building

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

Bay Club Hotel & Marina

Address: 2131 Shelter Island Drive, San Diego, CA 92106

Category: Moderate

Location: On Shelter Island

Notable Features: Superb views of the San Diego Bay, Bay Club Hotel Marina, and downtown skyline

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
  • Quarterdeck Restaurant and Bar – California-American style cuisine
  • Happy hour Monday through Friday from 4-7 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 $18 a night, only service animals are allowed at the hotel.

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The rest of the hotels on this list are near Shelter Island, either in Point Loma, Liberty Station, or west of the San Diego Airport.

5. The Pearl Hotel

Exterior of The Pearl Hotel San Diego
The Pearl Hotel (Josh Cho Photography – Pearl Hotel)

Address: 1410 Rosecrans Street, San Diego, CA 92106

Category: Budget/Moderate

Location: Near Shelter Island, 1.3 miles

Notable Features: The cool saltwater pool in the courtyard that’s a little social hub.

What. to Expect: A hip, modern boutique hotel near Shelter Island that won’t break the bank.

The Pearl Hotel, with its mid-century design and modern amenities, is located in the heart of Point Loma and offers 23 sustainably-minded rooms with local ceramics and original and vintage artwork. It’s also on our list of best budget hotels in San Diego.

Hotel amenities:

  • LCD televisions with HBO
  • Complimentary Wi-Fi
  • Certified organic Mooncloth X Casetta bath amenities
  • Finery X Casetta bathrobes
  • Terrace seating (in some rooms)
  • The famous oyster-shaped swimming pool
  • Onsite cocktail bar and Charles + Dinorah restaurant

Good to know: Want to take some of The Pearl home with you? The Casetta Shop offers on-site shopping, with several luxury items available. You can see the dive-in movie screen from The Pearl Jr. Suite’s balcony if you want to book that on dive-in movie nights.

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6. The Monsaraz San Diego, Tapestry Collection by Hilton

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Address: 1451 Rosecrans St, San Diego, CA 92106

Category: Budget/Moderate

Location: Near Shelter Island, 1.4 miles

Notable Features: Award-winning Humphreys So Cal Dining and Music and private marina

What to Expect: If you’re a Hilton Honors member who likes boutique hotels this is a fit. Since they take one pet up to 75 lbs, it’s a good option for large dog owners. You’ll find Portuguese-inspired decor — a nod to the area’s Portuguese community — mixed with mid-century modern.

Hotel amenities:

  • Complimentary Wi-Fi
  • Westerly restaurant, a favorite with locals
  • Fitness center
  • Minifridges, irons, and coffeemakers in rooms
  • 55″ TVs
  • Valet parking only

Good to know: They do not have a swimming pool.

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7. Best Western Yacht Harbor Hotel

Address: 5005 N Harbor Drive, San Diego, CA 92106

Category: Budget

Location: Near Shelter Island, 2.0 miles

Notable Features: Excellent location and complimentary hot breakfast

What to Expect: Ideal accommodations for the budget-conscious traveler. Newly revamped guestrooms boast a simple, modern charm.

Each room includes an attached balcony, a mini fridge, and a microwave. This waterfront budget choice has a good location across the street from Harbor Promenade.

Amenities:

  • Heated outdoor pool, sundeck, and Jacuzzi®
  • Fitness Center (Premium Precor fitness equipment)
  • Business Center (fees may apply)
  • Meeting facilities and conference services

Good to Know: Children 12 and under are free when accompanied by an adult, pets are not allowed, accessible parking and accessible rooms are available, free outdoor parking, free garage parking, and complimentary Wi-Fi.

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8. Homewood Suites by Hilton San Diego Airport-Liberty Station

Breakfast area at Homewood Suites Liberty Station

Address: 2576 Laning Road, San Diego, CA 92106

Category: Moderate

Location: Near Shelter Island, 2.7 miles

Notable Features: Airport shuttle and free hot breakfast 

What to Expect: Offering apartment-style living, this exclusively all-suite hotel provides fully equipped kitchens near the popular Liberty Station Public Market.

This includes a full-sized refrigerator, dishwasher, microwave, twin burner cooktop, and all the kitchen utensils you’ll need. Nearby attractions include Cabrillo National Monument, Downtown San Diego, and San Diego Zoo.

Amenities:

  • Suites have water, courtyard, or parking lot views
  • Outdoor pool and Jacuzzi tub
  • 24-hour fitness center with a few cardio and weightlifting machines
  • Basketball court
  • 24-hour business center
  • Meeting rooms
  • Onsite convenience store
  • Complimentary grocery shopping service
  • Lush grounds with a variety of outdoor seating areas, including firepits and outdoor grills
  • Complimentary evening reception with drinks Monday through Thursday

Good to Know: Non-smoking, self-parking and no valet, no electric car charging stations, pet-friendly rooms, accessible rooms and amenities, digital key suite entry, free Wi-Fi, and coin laundry.

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9. Courtyard by Marriott San Diego Airport/Liberty Station

Aerial view of Courtyard Marriott Liberty Station in San Diego near Shelter Island

Address: 2592 Laning Road, San Diego, CA 92106

Category: Moderate

Location: Near Shelter Island, 2.7 miles 

Notable Features: Waterfront business class hotel near the airport. Adjacent to a 46-acre park. Short walk to Point Loma’s cultural hub – Liberty Station Marketplace. 

 

What to Expect: Courtyard by Marriott San Diego Airport/Liberty Station is a waterfront hotel across from Liberty Station where guests can access restaurants, bars, shops, galleries, museums, and theaters.

The hotel offers contemporary, tech-friendly king and double queen guestrooms and king suites. It’s a good choice for overnight layovers, business travelers, and families who need a central location for San Diego’s many attractions.

Amenities:

  • Heated outdoor pool and spa tub, park and waterfront views, cozy fire pits
  • 24-hour fitness center, cardio, and weight machines
  • SUP Connection on the beach (standup paddle board and kayak rentals)
  • Bike rentals, and waterfront jogging/biking trails connect to Downtown
  • Free high-speed Internet, ergonomic workstation, Keurig coffee maker, signature bedding
  • Starbucks waterfront BISTRO
  • The Lounge restaurant/bar serving California cuisine
  • Fully equipped business center
  • Accessible rooms and common spaces, elevators

Good to Know: Ask for waterfront accommodations to avoid overlooking the parking lot. Paid self-parking, no pets policy, free airport/hotel shuttle, nonsmoking property, check-in 4 p.m./check-out 11 a.m., check website for current promotions.

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10. Hampton Inn & Suites San Diego Airport Liberty Station by Hilton

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Address: 2211 Lee Court, San Diego, CA 92101

Category: Budget

Location: Near Shelter Island, 2.9 miles

Notable Features: Free hot breakfast, digital room key, outdoor pool, water view rooms

What to Expect: Hampton Inn & Suites San Diego Airport/Liberty Station is a modern hotel between the airport and popular Liberty Station.

There are 181 rooms and suites within six categories: classic king, king water view, king studio suite, king studio suite water view, classic double queen, double queen water view. Clean, stylish hotel that’s great for families and couples ready to see the sights of San Diego.

Amenities:

  • Free hot breakfast
  • Free Wi-Fi
  • Nonsmoking rooms
  • Complimentary hotel/airport shuttle
  • Outdoor heated pool
  • Fitness center
  • Business center
  • Pet-friendly rooms

Good to Know: check-in 3 p.m./check-out noon, accessible rooms, paid self-parking, pets allowed with deposit, electric vehicle charging

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11. Ramada by Wyndham San Diego Airport

Ramada by Wyndham San Diego Airport

Address: 1403 Rosecrans Street, San Diego, CA 92106

Category: Budget

Location: Near Shelter Island, 1.8 miles

Notable Features: Overlooks Americas Cup Harbor and Shelter Island.

What to Expect: Ramada by Wyndham San Diego Airport is an unassuming, casual hotel with 80 rooms. King, double queen, one-bedroom double queen suite, two-bedroom double queen suite accommodations are available. This hotel is a good choice if you just need a clean, comfortable place to sleep with free parking and a free, quick breakfast before you head out to see all that San Diego has to offer.

Amenities:

  • Outdoor pool and sun deck
  • Fitness center
  • Business center
  • Mini-Mart
  • Free hot breakfast buffet
  • Walk to downtown
  • 5-minute drive to several San Diego attractions
  • Free Wi-Fi
  • Some rooms/suites have private balconies and water views

Good to Know: Up to 2 kids under 16 stay free with an adult, airport/hotel shuttle and hot breakfast are free, complimentary cribs/infant beds upon request, many rooms are accessible, smoking and nonsmoking accommodations, free parking, check-in 3 p.m./check-out noon

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12. Comfort Inn San Diego Airport at the Harbor

Address: 5102 N Harbor Dr., San Diego, CA 92106

Category: Budget

Location: Near Shelter Island, 1.9 miles

Notable Features: Complimentary Wi-Fi and hot breakfast, economical, comfortable

What to Expect: Hotel Comfort Inn San Diego Airport at the Harbor is a straightforward, casual choice of accommodations. There are a few options for your stay, king, double double, double queen, king plus double suite, and king with bunkbed. The hotel’s 46 rooms have been recently updated and have engineered wood floors, refrigerators, work desks, and microwaves. Wi-Fi is complimentary. Choose this hotel if you’re going on a fishing trip, a cruise, or plan to spend most of your time adventuring in San Diego and need a comfortable place to lay your weary head. 

Amenities:

  • Free hot breakfast buffet
  • Outdoor pool and sun deck
  • Complimentary newspaper weekdays
  • Amenity gift upon arrival
  • Express check-in/check-out
  • Range of restaurants within walking distance

Good to Know: Paid parking, paid hotel/airport shuttle, nonsmoking property, no dining onsite (other than breakfast buffet), accessible rooms available

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13. Holiday Inn San Diego Bayside, an IHG Hotel

Holiday Inn San Diego - Bayside

Address: 4875 N Harbor Drive, San Diego, CA 92106

Category: Moderate

Location: Near Shelter Island, 2.3 miles

Notable Features: 9-hole mini golf, some suites have balconies, tropical landscape, restaurant

What to Expect: Holiday Inn San Diego Bayside, IHG Hotel is a lovely hotel on a bayside property with lush, tropical landscaping. Guests choose from a variety of rooms and suites, some with balconies, some ground floor with outside access, and some with bay views. King suites and double queen suites have sofa beds. There are also king guest rooms and double queen guest rooms. The hotel is family-friendly with lots to do on the property.

Amenities:

  • Free Wi-Fi, minifridge, coffeemaker
  • Suites add separate bedroom, microwave, sofa bed
  • Some suites have balconies
  • Free loaner bikes
  • Outdoor pool, sundeck, and spa tub
  • Fitness center noon to 11:45 p.m.
  • Table tennis
  • Shuffleboard
  • Complimentary 9-hole mini-golf
  • 24-hour business center
  • Point Loma Café – breakfast, lunch, dinner, weeknight happy hour, kids eat free (11 & under)
  • Bayside Bar – Happy Hour 5 p.m. to 7 p.m., indoor/outdoor seating, patio firepits
  • Mini mart

Good to Know: Paid self-parking, paid breakfast, check-in 4 p.m./check-out noon, complimentary hotel/airport shuttle, accessibility features in rooms, suites, and throughout the hotel, kids 18 & under stay free in parents’ room, no pets

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

Exterior view of TownePlace Suites at Liberty Station near the Airport.

Address: 2311 Lee Court, San Diego, CA 92101

Category: Budget

Location: Near Shelter Island, 2.9 miles

Notable Features: Designed for long stays; walking distance to the airport, downtown, and Liberty Station. 

What to Expect: TownePlace Suites by Marriott San Diego Airport/Liberty Station opened in 2019. The simple elegance of the nautical aesthetic combines with design functionality to make this hotel the perfect choice for long stays.

They offer studios, one-bedroom, and two-bedroom suites with kitchenettes, their signature Home Office Suite built-ins, and Container Store custom elfa storage closets. Live, work, and play with minimal disruption from routine at this business-friendly, family-friendly option.

Amenities:

  • Residential atmosphere with kitchenettes
  • Adjustable workspaces with Home Office Suite
  • Custom elfa closets
  • Complimentary hot breakfast
  • Outdoor Weber grills
  • 24-hour mini market
  • On Us coffee/tea service
  • Outdoor heated pool
  • Outdoor lounge area with casual seating and fire pit
  • 24-hour fitness center
  • Complimentary airport/hotel shuttle service
  • Complimentary Wi-Fi
  • Business services
  • Laundry facilities

Good to Know: Pet-friendly (2 pets, total 50 pounds, deposit), no restaurant onsite, check-in 4 p.m./noon check-out, smoke-free property, fully accessible, onsite paid parking, electric car charging station, contactless mobile payments, check website for current promotions

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Do you have favorite Shelter Island San Diego hotels?

Katie Dillon is the managing editor of La Jolla Mom. She helps readers plan San Diego vacations through her hotel expertise (that stems from living in a Four Seasons hotel) and local connections. Readers have access to exclusive discounts on theme park tickets (like Disneyland and San Diego Zoo) and perks at luxury hotels worldwide through her. She also shares insider tips for visiting major cities worldwide, like Hong Kong, London, Paris, and Shanghai, that her family has either lived in or visits regularly (or both).

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