8 Best Mission Beach Hotels and Mission Bay Hotels in San Diego

Basing a San Diego vacation at one of our Mission Beach hotels or Mission Bay hotels has many benefits, but it’s important to understand the location you’re booking into clearly. These adjacent neighborhoods are referred to interchangeably, despite their different beach experiences, which I find tends to confuse travelers.

We’ll discuss the two different beaches here — bay and ocean — and go over which hotels provide access to one or both. I’ll also where why people stay here (or don’t) so that you are fully informed when you book.

Where Is Mission Beach?

Mission Beach is a coastal San Diego neighborhood bordered by Mission Bay to the east, Ocean Beach to the south, the Pacific Ocean to the west, and Pacific Beach to the north.

When researching Mission Beach San Diego hotels, you may also generate search results that include Pacific Beach hotels.

This is because the dividing line between Mission Beach and Pacific Beach is not well marked on maps. Not many San Diegans can tell you exactly where it is either because both neighborhoods share the same zip code.

For this reason, I included a few south Pacific Beach hotels on this list near the action in Mission Beach or border Mission Bay.

Where Is Mission Bay?

Mission Bay is a human-made saltwater bay that includes a 4,600 square-foot aquatic playground — which happens to be the largest of its kind in the world. 

It’s bordered by Mission Beach to the west, Pacific Beach to the north, the I-5 freeway to the east, and various San Diego neighborhoods to the south. Mission Bay’s roughly 4,325 acres are half land and half water with 19 miles of bay beach surrounding the water.

West Mission Bay is mostly in Mission Beach, but East Mission Bay might be Pacific Beach, for example. (If your family is looking for hotels near SeaWorld San Diego, this famous attraction is located on Mission Bay, too.)

See also: Best Beachfront Hotels in San Diego

Reasons to Stay in Mission Beach and Mission Bay Hotels

Let’s talk about why you would stay in this part of San Diego, California.

Convenient Location

Most Mission Beach hotels and Mission Bay hotels are less than 5 miles from the San Diego International Airport, making them highly accessible for travelers.

Local hotels and resorts are good for travelers who want quality California beach time while remaining close to downtown San Diego.

Lower Prices

This area is more casual, and usually, accommodations cost less than Del Mar or La Jolla beach hotels. There are also some great family resorts that I’ve also featured on my list of best kid-friendly San Diego hotels.

One important thing to note is that these hotels do not usually suit luxury travelers. If you want a truly five-star experience, read best San Diego luxury hotels.

Two Different Beaches

This part of town offers two different beach experiences. The beaches of Mission Beach have beautiful white sand with great waves to surf and a fun boardwalk full of restaurants, shops, and even a beachside amusement park (Belmont Park) with casual Mission Beach restaurants.

The other beach surrounds waveless Mission Bay. The calm waters here are good for young kids (it can be murky in spots though) and water sports enthusiasts who want to do everything from waterskiing to riding aqua cycles.

Some hotels on this list are not walkable to the ocean beach, while others are. Without further ado, here are my favorite Mission Beach hotels and Mission Bay hotels in San Diego.

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1. Hyatt Regency Mission Bay Spa & Marina

Location: Bayfront on Mission Bay and four blocks from Mission Beach (20-minute walk)

Families love this 4-hotel as it’s the only one in San Diego with multiple water slides. Hyatt Regency Mission Bay Spa and Marina is four walkable blocks from Belmont Park and Mission Beach.

There are multiple renovated room styles available, including ones with an ocean view, marina view, rooftop terrace access, and suites.

Good to Know: It takes two minutes to drive over to SeaWorld San Diego. They do not have a Regency Club level.

Reservations:

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2. San Diego Mission Bay Resort

Location: Mission Bay

San Diego Mission Bay Resort was recently renovated and entered into the Noble House Hotels and Resorts portfolio. It was formerly the Hilton San Diego Resort. Guests like the elevated but still casual experience, and I am a fan of the new, lighter coastal room decor.

It’s a great option for families who intend to explore Mission Beach and other parts of San Diego, as the resort is next to the freeway. The Mission Bay boardwalk is right in front of the hotel, as is a nice sandy bay beach.

There are also seasonal bonfires and s’mores nights. There is an amenity fee (currently $38/night) that grants you unlimited access to Wi-Fi, the fitness center, the pool, the tennis courts, board games, resort games, and more.

Some rooms have outdoor fire pits for cozy nights and s’mores (I’d recommend these).

Beach Amenities

• The Sandbox rents bikes (surreys, beach cruisers, kids bikes, and trailers) to ride on the boardwalk and sand toys for use on the beach
• Action Sports Rentals at the resort marina rents electric catamaran lounge chairs, bikes, stand-up paddleboards, wave runners, and more
• There is a beach volleyball net (balls are available from the front desk)

Hotel Amenities

• Choose between guest rooms, studios, and suites (some have bay views), all with luxury bedding, small refrigerators, and private balconies or patios
• Waterfront pool and wading pool for young kids
• Poolside cabana rentals and menu service
• Two dogs up to 75 lbs are welcome (additional fees apply)
• A nice market and boutique with plenty of grab-and-go food and wine for the room
• Fire pits in some rooms (s’mores kits are available in the market)
• Waterfront dining at Covewood Restaurant
• Full-service spa
• Championship tennis courts
• Seasonal dive-in movies
• Game rentals at the front desk

Good to Know: Like Paradise Point, the San Diego Mission Bay Resort is on the opposite side of Mission Bay from the sand at Mission Beach. It is about a 4-mile scenic car ride around the bay. The upshot is freeway access is easy here. You may also buy a pool day pass through ResortPass.

Awards: TripAdvisor Certificate of Excellence and GreenLeaders Silver Level (for eco-friendly practices)

Reservations:

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3. The Catamaran Resort Hotel and Spa

Location: Mission Bay but a few blocks from Pacific Beach

The Catamaran Resort Hotel and Spa offers the most amenities of any Mission Bay hotels (though technically located in Pacific Beach), from a fantastic spa loved by locals to a picturesque and perfect bay location. 

The Pacific Ocean beach is also a few minutes walk across the street. It’s easy to explore the area by bike, which you can also rent at the resort.

The resort is tropical in style, so it almost feels like stepping into Hawaii. Dining is excellent, especially at the signature restaurant, Oceana. There are on-property activities to take advantage of, ranging from seasonal sunset luaus to chatting with the resort’s resident macaws.

Beach Amenities:

• Seasonal stand-up paddle board (SUP) yoga on the bay
• Summertime luaus and beach movies
• Beachside yoga
• Surfing, sailing, and SUP lessons, in addition to kayaks and wakeboarding rentals onsite
• Beach chairs and umbrellas for guest use
• Beachfront restaurant

Resort Amenities:

• Each guest room and suite has a private balcony or patio and water or tropical water views.
• Studios have kitchenettes
• The resort’s Bahia Belle Sternwheeler boat takes guests on family hour and cocktail cruises
• A fantastic spa based on Polynesian, Thai, and a variety of other South Pacific traditions
• Bicycle rentals on site
• Complimentary arcade
• Tropical bird show with resident birds
• Turtles and ducks to look at in the various tropical water features

Good to Know: This is a very popular choice for families. It’s an awesome location for taking advantage of both bay and ocean beaches while also being within walking distance of Pacific Beach restaurants.

These are not fancy accommodations by any means. The buildings look a bit run down on the exterior, but rooms have recently been refreshed with new Keurigs, beds, and decor.

Awards: TripAdvisor Certificate of Excellence and Traveler’s Choice in 2022

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4. Bahia Resort Hotel

Location: Mission Bay and a 10-minute walk to Mission Beach

Bahia Resort Hotel was the very first Mission Bay hotel. The Mediterranean-themed resort is located on a secluded 14-acre peninsula that juts out into the bay and has its own private bay beach.

To get to the ocean at Mission Beach, guests must walk an easy 10 minutes. The walk passes Belmont Park, San Diego’s beachfront theme park, and drops you at the beach and boardwalk. It’s a sister property to The Catamaran Resort Hotel and Spa, which means there is transportation between the two properties.

On-site dining options include a signature restaurant (Dockside 1953) and the Airstream Grab N’ Go café. A secluded beach connected to the resort makes for easy lounging and sunset watching.

Beach Amenities:

• Private bay beach
• Rentals of wetsuits, boogie boards, rafts, paddle boats, kayaks, powerboats, wave runnerss/sea-dos
• Seasonal summer beach concerts and clam bakes
• Complimentary cabanas
• Seasonal kids’ beach activities

Resort Amenities:

• 314-rooms which include beach-front cottages, studios with panoramic views, and spacious bayside suites
• Bayfront suites have direct beach access, and Studios offer full kitchens and dining areas
• Driver service to The Catamaran Spa
• Two complimentary lighted tennis courts
• Heated swimming pool with Jacuzzi
• The Bahia Belle Sternwheeler boat, which takes guests on family hour and cocktail cruises
• Pond with ducks and rescued seals (kids will love them)
• No resort fees and complimentary parking
• A Moroccan-inspired lounge with live music
• Fitness center

Good to Know: The hotel has a reputation for fantastic service and is popular with those looking for a more wallet-friendly choice with good beach access. Guests here use the spa at The Catamaran.

Awards: TripAdvisor Certificate of Excellence, voted a Best Value Hotel in America by TripAdvisor

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5. The Dana on Mission Bay

Location: Mission Bay

The Dana on Mission Bay is a casual, low-key hotel that also welcomes guests with a tropical atmosphere. It is actually the closest hotel to SeaWorld San Diego and about a mile to the heart of the action in Mission Beach. The 10-acre resort has two main buildings: Marina Cove and Water’s Edge.

The Firefly Eatery & Bar is an on-site American-style restaurant with a unique cocktail list and daily happy hour.

Beach Amenities:

• Adventure Water Sports rentals, which include wave runners, powerboats, paddle boats, bicycles (singles and tandems), ski boats for waterskiing and wakeboarding, paddleboards, and kayaks.
• Seasonal youth classes where kids can learn water sports

Resort Amenities:

• Flat-screen HDTVs, refrigerators, microwaves, and single-cup coffee and tea makers in all rooms
• Wet bar, hand-crafted furniture, balconies, and patios, water views in Water’s Edge section
• Up to two dogs per room are welcome (80 lbs maximum, additional fees apply)
• Firefly restaurant is also pet-friendly
• Bayview infinity pool and spa; tropical pool and spa
• Onsite restaurant and seasonal pool bar
• Private marina with boat slips for hotel guests (reservations necessary)
• Laundry facilities
• Seasonal dive-in movies
• Lawn games

Good to Know: As mentioned above, the ocean beach at Mission Beach is about a mile away, but you can walk or ride a bike there. It is an older property but also can be a great value for money. You can bundle your room with SeaWorld San Diego and other theme park tickets in a vacation package.

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6. Paradise Point Resort and Spa

Location: Mission Bay

This secluded tropical resort experience is great for families. Paradise Point Resort and Spa is a 462-room bungalow-style resort set on Mission Bay established in 1962 by famous Hollywood Director Jack Skirball. The 44-acre resort actually feels like a secluded tropical island.

Over one mile of beach circles the resort with its five swimming pools, tranquil lagoons, and lush gardens.

The bay beach here is a fun San Diego beach for kids, and they do swim here (the water can be murky). The ocean beach at Mission Beach requires a 2-mile drive around the bay to get there.

Beach Amenities:

• Bonfire pits
• Beach games like volleyball, bocce ball, and horseshoes
• Beach toys and accessories available for purchase at the Island Market
• Paradise Surf Academy

Resort Amenities:

• Five swimming pools, including an adults-only pool
• 462 Balinese-inspired bungalow rooms, including 73 suites with private patios, mini-refrigerators, and in-room coffee (suites have wet bars and microwaves)
• A full-service marina with sailboats and ski boats
• Wakeboarding, waterskiing, kayaks, paddleboats, and fishing
• 18-hole putting golf course
• Five dining venues, including two waterfront restaurants
• Award-winning, island-themed spa with kids’ treatments
• NBA-sized basketball court and tennis courts
• Pet-friendly to 15 lbs or less (fees apply)
• Kids Zone family activities year-round
• Duck and fish feedings in the lagoons (duck and fish food is available at Island Market)
• Skateboarding lessons

Good to Know: The hotel is expected to be transformed into the Margaritaville Resort San Diego in 2024 after a $35-million renovation. The new resort will have 80,000 square feet of event space, signature Margaritaville-style bars and restaurants, and 73 suites among its 462 rooms.

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7. The Wayfarer San Diego

Location: Beachfront on Mission Beach

Formerly known as the Blue Sea Beach Hotel, The Wayfarer is a Pacific Beach hotel on the border of Mission Beach that offers ocean views, pool access, and newly upgraded guest rooms and suites. 

Close access to the boardwalk and beach make it a great choice for anyone that wants to spend their days with their toes in the sand.

Recent renovations include upgraded rooms with surfer-chic decor and a new on-site café. The lobby is still undergoing renovations and will feature a sleek, modern decor with a classic San Diego beach vibe.

Resort Amenities:

• 118 rooms and 8 suites
• In-room coffee machine, mini refrigerators, 50-65″ flat-screen TVs, free local calls, luxury bath products, and complimentary WiFi
• Most rooms have ocean views
• Rooms with sofa beds available 
• Easy access to the Strand
• Seasonal on-site surf lessons
• Oceanside pool deck
• 24-hour business center
• Grab-n-go pantry in lobby
• Year-round heated pool and spa
• Beach Cruiser bike rentals

Good to Know: The beach is busy here and tends to skew a bit younger, but guests report that noise is low in rooms away from the street.

Awards: TripAdvisor Hall of Fame

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8. Surfer Beach Hotel

Location: Beachfront on Mission Beach/Pacific Beach border

Surfer Beach Hotel is in Pacific Beach, steps from the border of Mission Beach. The no-frills hotel sits beachfront on the boardwalk, which means that views are spectacular and ocean breezes are guaranteed.

Rooms are comfortable and clean. The World Famous PB restaurant is next door, which equals easy access to great fish tacos and casual beachfront dining. The building is older, but this is certainly one of the most affordable beachfront hotels in the area.

Hotel Amenities:

• Family rooms can sleep up to 6 people
• Suites with kitchens and separate living areas are available
• In-room coffee and microwaves are available in some rooms
• Complimentary wireless internet
• Complimentary hot beverages in the lobby
• In-room mini refrigerator
• Ironing boards and hair dryers on request in standard rooms
• Heated ocean view swimming pool
• Pets less than 50 lbs are welcome (maximum two per room and additional fees apply)
• Coin-operated laundry machines
• An activity desk
• Safe deposit available at front desk

Good to Know: There are incentives for booking directly through the hotel, but you can also save if you bundle theme park tickets with your booking in a vacation package.

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What is your favorite Mission Bay hotel?