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 : I mention hotel booking resources I know offer the best prices via membership programs or ones that are popular with readers. Mentioned pricing and amenities are subject to change. If you book through links on this page, I may earn a small commission.
1. Kona Kai Resort & Spa
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
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
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
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
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
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 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
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
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
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
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
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
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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