Update: On August 19th the Yellowstone River was temporarily shut down from the Yellowstone Park boundary to Laurel, MT due to the discovery of a parasite that is responsible for the death of whitefish and some trout. Please contact your local fly shop or Montana Fish, Wildlife and Parks for the most up to date information regarding the closure.
September 1st: Yellowstone River below 89 Bridge has been reopened to fishing and recreation including it's tributaries, except the Shields River. Carbella to 89 remains closed to all recreation, but all tributaries that feed into the Yellowstone within that section are reopened. Read this for more info.
Phew...what a summer! As we move into September river traffic lightens up significantly, water and nighttime temperatures start to fall and brown trout start their mating dance.
The Gallatin will experience few hatches of aquatic insects this time of year, but expect to see some fall baetis and midges milling around still with the occasional caddis here and there. Hoppers and ants will remain relevant as well, but as the mercury starts to plummet fewer bugs will be moving around. Try stripping larger hoppers in fast water along sun baked banks, or swinging some streamers and of course nymphing will always produce some fish. Carnage Hoppers, Sheila's Sculpins, Lightning Bugs, RS2s and Zebra Midges are good patterns to consider.
The Madison will receive the most attention from fall anglers. Mostly in walk wade areas, such as in Yellowstone National Park, in between Hebgen and Quake Lake and the Raynold's and $3 Bridge. The park has sort of a cult following this time of year. Some will line up for their turn in Baker's and Barnes holes, while others will hike in and find a bit more solitude and swing streamers and soft hackles or nymph with eggs, worms and small baetis patterns. In between the lakes or below Quake Lake will usually offer more solitude and the fishing can be just as good if not better at times. You may have a better chance of hooking into that 20+ incher in the park that has moved up from Hebgen Lake though.
Whatever your goal this September please be especially carefully to Clean, Inspect and Dry all of your gear when moving from one body of water to another. This could prevent the transfer of parasites like proliferative kidney disease (PDK) that has been discovered in the Yellowstone River.