- Balboa Park: There are at least three public restrooms in Balboa Park. They probably close at sunset. I have been to two of them. The one by the tennis courts is much nicer than the one by the ball fields. This is quite a hike from the areas I generally spend my days. I am currently on foot. If I get a bus pass, this might be more relevant to me.
- Embarcadero/ The Waterfront: I have yet to find an actual beach. The waterfront here is basically part of downtown and is very developed. There is a map somewhere on the waterfront showing some of the public restrooms. I don't think it shows all of them. I have found three so far, of varying degrees of quality. They probably all close at sunset. I fairly often go to the waterfront to use the restroom. Some of these bathrooms have hot air hand dryers.
- Neil Good Day Center: If you are a member here, you can use the bathroom here from 6:00am to 4:00pm on weekdays and until 2:00pm on weekends and holidays. The ladies room has only one toilet, you frequently have no privacy while on the toilet, and the hand dryer blows cold air after holding the button down for several seconds. If I were a billionaire, I would pay to get a functional hand dryer and add a second toilet for the ladies.
- St. Vincent's: There is a bathroom which is definitely available during the free meal they do daily (lunch Monday through Saturday, breakfast on Sunday). I asked and was told it is available all day and sometimes at night but I have gotten funny looks from security when I went later in the day and someone who was with me was asked if they were residents and told to leave. So I try not to go too often at non-meal times and I try to kind of quietly sneak in.
- God's Extended Hand: There is a bathroom available during meal times but not other times. Update: I have never used them, but they also seem to have 4 portapotties at Island and 17th. I am guessing these might be open 24/7 but I do not actually know.
- Salvation Army: Bathroom available there if you eat dinner there.
- The Zoo: I overheard someone say he got an annual pass to the San Diego zoo and he goes there to use their bathrooms. I can't afford that right now and I think it would make a lot more sense with a bus pass, which I do not yet have but he clearly does.
- Central Library: The library used to be at 8th and Broadway. There is a new central library. I have never been there. I assume they have public restrooms. Word on the street is that they are trying to figure out how to keep the homeless out.
- Trolley Station: The station at 12th and Imperial has a public restroom. It is not open on weekends. I have been told it is open Monday through Friday from about 7:00am to about 5:30pm. You do have to go through security to access it.
- 3rd and C: Public restroom and it is open 24 hours. No hooks to hang anything but it has an awesome hot air hand dryer in the ladies room. Edit: The last few times I went, the awesome hand dryer was blowing cold air only.
- Horton Plaza: This is a five story open air mall on 4th Street. There are outdoor escalators at 4th and E but it takes up a couple of city blocks or more. My recollection is that there are three restrooms when it is open.
If you leave downtown San Diego, some good places to look for public bathrooms are beaches, malls, public libraries and federal or state public facilities. As an example of a state public facility, Torrey Pines State Park has public bathrooms. Most of these will basically be open only during the day and will close at night. It is common to see a notice that says something like "Open 7am to 7pm" or "Open Sunrise to Sunset."