What you have to watch out for are city limits, ownership/management of the body of water, and wildlife refuges.
San Diego Bay is probably considered within the city limits, and it contains wildlife refuges. Mission Bay is probably within city limits as well.
Otay Lake is owned by a water district, and used to allow hunting, but not any longer.
Barret and Sutherland are also owned by water districts, and they do allow hunting.
Loveland and Sweetwater are owned by the Sweetwater Authority, and allow fishing in small portions of the lakes, but not hunting. I've seen pictures of Babe Ruth hunting Sweetwater back in the day, and I can tell you that ducks and geese use it every year. Can't hunt it though.
Salton Sea is open to hunting EXCEPT within the boundaries of the Sonny Bono Wildlife Refuge. There are maps, but knowing where that actual boundary is would be difficult or impossible. I think most guys that hunt the sea just do their best using the maps they have.
I think if you have an AZ hunting license, you can hunt the Colorado River just about anywhere that it doesn't go thru city limits.
Others can correct me where I'm wrong.