I live in Des Moines IA and fish the Driftless a half dozen or so times a year. Can't comment on the Root River in MN because the fishing is so good in the Decorah area, I can't see driving that much further.
September is a good time to fish that area. Although, you might find low water, the streams are still fishable. I primarily fish North Bear and Waterloo. North Bear is near the Highlandville area, which is north of Decorah and Waterloo is near Dorchesterm which is also north of Decorah. Both streams have brown, rainbow and brook trout. The browns and brookies do reproduce and the rainbows are stocked. There is a section of Waterloo just below Dorchester that is catch and release only.
These streams, like all the streams in the Driftless are spring creeks. You will find good bug hatches throughout the year. I was up there the end of April (going again this weekend) and had great dry fly fishing. There had been a Hendrickson hatch so the trout were zeroing in on larger Adams patterns. Caddis are now coming off and terrestrials are just beginning to appear. You can also nymph just about 12 mos out of the year and catch fish. If you go to the Iowa DNR website, you can get more information, along with a weekly fishing report. Also, you go to streamfishingiowa.com. This is a good site for information on what's happening. There is also a guide service; Northeast Iowa Fly Fishing, in case you are interested. You can google to find their site and blog. If you want to get into some technical fishing, then be sure to check out French Creek, near the dairy farm.
Most guys I know fish either an 8 1/2' or 9' 4wt rod with either a wf or dt floating line. Some typical patternw would be Para Adams 14-20, EHC 14-18, Griffiths Knat 18-20, GRHE 14-18, American Pheasant Tail 16-20, Leadwing Coachman 12-16 and Woolly Buggers 6-12.
I also fish around the Manchester area from time to time. There is a hatchery there at Spring Branch Creek. I fish here mostly in the colder months since it is a closer (3 hour) drive. It has great midge fishing. The stream is small and clear and will test your skills as an angler. No other stream has humbled me from time to time like Spring Branch. I also need to mention that there is a silting problem going on due to some farmer up stream not keeping his cattle under control.
I should also mention that if you do go to the Highlandville/Dorchester area, a great place to stay is Sportsman's Motel right out side of Dorchester. The rooms are clean and comfortable and the price is very reasonable. I think around $40 a night. There is also a small cafe where you can eat breakfast.
Last edited by anglerdave; 06-04-2013 at 02:16 PM.
" If a man is truly blessed, he returns home from fishing to the best catch of his life." Christopher Armour