Of these hotels, which is the best place to stay in San Diego: Humphrey's, Catamaran, or Bahia? It will be the first trip to San Diego for my husband and I. We want a hotel that is comfortable, clean, has amenities, is close to the water, and not in an downtown setting.

what time of year are you coming? Humphrey's is really nice but in the summer they have outdoor concerts which some people may not enjoy the crowds or the music. Humphrey's is a really nice hotel and is on shelter island. it is on the San Diego Bay and i really like the location.
The Catamaran and the Bahia are owned by the same people., both of those are on mission bay but you could walk across the street to the ocean. so if you want to be able to walk to the pacific ocean i would go for the Catamaran first and then the Bahia. i've never been but i hear the Catamaran has a very nice spa too.

Stayed at Loews Coronado Bay last Summer and it was very nice; got a great deal on priceline. Walked alond the beach a while.

The little town of Coronado nearby was nice to walk through, lots of little shops and restaurants.

In Coronado there's the historic Hotel del Coronado; we walked through it, the bellhops still wear the old fashioned uniforms with caps.

Sorry, don't know about the hotels you mentioned but I hope this helps nonetheless.

Just in case you'd be interested in the concerts at Humphrey's no matter where you stay, here's the schedule for this summer:



http://www.humphreysconcerts.com/

We have stayed at the Bahia and the Catamaran. Catamaran was nice and could walk to the ocean as stated above, but my favorite place we have stayed is the Pacific Terrace Lodge (near the Catamaran, but right on the ocean) or Sea Lodge, which is up in LaJolla right on the ocean. Being on the bay is okay, but can't compare to being on the ocean!