Keep the filtering options; those are pretty cool. When I say "drainage separator bar" I just mean some visual way of separating the drainages on the list (that only shows when sorted by drainage). In the old setup this was a gray bar across the page between the last run of one drainage and the first run of another. A couple of black lines or a change in text color would also do the same thing.
Sorting by flows would be awesome but, as you said, there are a couple of things that make this a little tricky. One of the big issues is that you can't just list them by cfs because you will have runs like Westwater that are low at 2500 while runs like Blackrock that are raging at 2000 are listed lower. It seems to me that the best way to do it would be to sort so that all of the runs listed as High show at the top, followed by Medium, Low, etc. Then within the block of runs listed as High, you could sort those by cfs/gauge height.
"The world would be a better place if everyone kayaked."-Brad Ludden (Valhalla)
"You only get one chance to run a drop blind."-DD