My husband and I are planning a 7 day trip to the Banff/Lake Louise area in September. We are planning to start the trip with 2-3 nights at the Rimrock Hotel in Banff and end with 2-3 nights at the Post Hotel in Lake Louise. Are there any recommendations for a bed and breakfast, inn, or another nice hotel that is less expensive to stay in between the two? Also, we were thinking of a whitewater trip as a one day excursion? Any thoughts or experience with this one? We are both outdoor enthusiasts. Are there any "can't miss" activities in the parks (or the town)?

I would stay at Emerald Lake Lodge which is more secluded--I think it would be very beautiful in September. There is a nice trail around the lake and you can rent canoes. Restaurant is very good.
We haven't done the whitewater trip because they want you to sign a waiver that says, basically, if you die or are permanently injured, even if it's our fault, we're not responsible. My husband, the attorney, refused to sign--he said, in the US, he would have because those kind of clauses aren't enforceable in court, but he didn't know enough about Canadian law.
We enjoy the hiking around Lake Louise, esp up to the teahouses. I like to shop in Banff.

Forgot to add--the Rimrock is one of our favorites--you'll have a great time.

there are cabins at johnson's canyon which is about 1/2 way in between but i personally wouldn't switch hotels just for 1 night for locations that are only about 1 hour apart.

I agree with ltt - it doesn't seem worth the bother to switch hotels when Banff and Lake Louise are so close (a 45 minute drive).

However, if you are still so inclined, I would suggest Baker Creek Chalets, lovely and comfy cabins or units in the main lodge, in the woods by a creek (hence the name), and only 8 minutes from Lake Louise on the Bow Valley Parkway (the road that long ago used to be the Trans Canada).