What color was the bug that you saw?  I've seen little yellow stoneflies on the creek.  Others have claimed to have seen salmonflies.  Once, I saw what I thought was a huge stonefly.  When I got home, I looked it up and found that it was a snakefly.  Both fold their wings over their back in the same manner, but the snakefly is not aquatic.     

I did a stream ecology project once for a biology class where a group of us gathered benthic invertebrates from a small creek.  We ended up with a lot of scuds, mayfly nymphs, caddisfly larvae, and midge larvae.  We even found a few damselfly nymphs, dragonfly nymphs, hellgramites, leeches and stonefly nymphs.  There weren't very many stoneflies, but they were there.  I'm sure that they're in Putah as well, but as far as numbers go, I don't think that there's too many of them.  I'll bet Bono would know more about the insect populations in Putah Creek due to the surveys that he's done. 

I would assume the fly that Mr 101fish saw was the Little Yellow Stone or the Little Yellow Sally(same thing).I normally see these in the spring thru mid summer on Putah and mainly near access #5 also up above access #1.I did see one last Sunday morning @ access #5.Ireally started seeing these stoneflies at Putah about 7 or 8 years ago after some very high flows cleaned the creek of its siltier areas,and made it more stonefly friendly.