Not many hotels have their own marina, but the Best Western Island Palms makes full use of its beautiful location on Shelter Island, in the middle of San Diego Bay. Boats line the waterfront to the rear of the hotel, while on the other side is the open expanse of the bay - all 174 rooms have great views of the water, and are clean & well equipped, if a little on the small side. All day dining is available on site at the waterfront Blue Wave Bar and Grill, though the island has at least 6 other restaurants, all within easy walking distance, or reachable on the free bicycles provided by the hotel. The complex also includes two outdoor pools, an exercise room, spa, and banquet/meeting space for up to 175 guests.

One of ten Holiday Inn hotels in the San Diego area, the Bayside inn is an older building 200 feet from the north edge of San Diego Bay, overlooking the marina, in a generally quiet area close to the US Naval Training Center. The hotel is situated along N Harbor Dr, a road which passes the airport after 2 miles and the downtown San Diego 2 miles further; the many other nearby attractions include Sea World a short distance north and Cabrillo National Monument to the south. The 237 rooms are divided into several blocks arranged around a sizeable garden area containing an outdoor pool, whirlpool, a 9 hole putting course, and many palm trees. Free parking and a free airport shuttle are available, plus other services of a restaurant, gift shop/newsstand, fitness center, games room, and 10 meeting rooms (4,805 sq ft of event space).

Formerly known as Best Western Posada Inn, this hotel has a new name, new management and a full renovation, to be finished in spring 2008. Most of the 111 rooms, on 6 floors, overlook the marina at the north edge of San Diego Bay - the hotel is located alongside N Harbor Blvd next to the Holiday Inn, about a 3 minute walk from the water's edge. The neighborhood contains a mixture of shops and restaurants near the bay then houses further back, with the US Naval Training Center just to the east; the best nearby place to eat seems to be Pizza Nova, a full service Italian diner just across the road. The hotel offers the usual amenities of free continental breakfast, outdoor pool, hot tub and exercise room.

Many of the 200 guest rooms at the newly built (open summer 2008) Courtyard San Diego Airport/Liberty Station have fine views over San Diego Bay - the hotel is part of a shopping center facing part of the waterfront, just off Harbor Drive and at the edge of the new Liberty Station development. The international airport is 2 miles east, with downtown San Diego 2 miles further. The hotel occupies a spacious site, surrounded by gardens and a short walk from a waterside park, and its many amenities include a restaurant, lounge/bar, picnic area and a cafe overlooking the bay. There are good meetings facilities - 5,000 sq ft of event space, and a business center. Parking is free (though not breakfast), and leisure amenities comprise an outdoor pool, whirlpool and fitness center.

The best aspect of Quality Inn San Diego Airport/Sea World Area is the location - the hotel is just 0.3 miles from San Diego Bay and the harbor, and a short drive from I-5 which puts all other San Diego area attractions within easy reach. The airport is 2 miles east (free shuttle available), and Sea World is 3 miles north. The hotel itself is quite an old, mid rise building of 110 rooms, many with nice views southwards over the ocean. Facilities are somewhat limited - there is no free breakfast available, but the hotel does have a pool, hot tub, sun deck, plus an on-site restaurant/bar.

The 2 storey Comfort Inn at the Harbor provides budget motel accommodation, but still with a good location, about 300 feet from the edge of San Diego Bay and 2 miles east of the international airport. The inn has 45 smallish rooms linked by exterior corridors, and an outdoor heated pool next to lawns, palm trees and a sundeck. Most of the central San Diego attractions are within 5 miles; for those not driving there is a bus stop right next to the hotel, on Rosecrans St. Free breakfast is served and there is a good selection of nearby restaurants.