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The CnR section starts above Eagle Cliff Bridge. The bridge is located at the top end of Swift Reservoir. I would focus my fishing to the mainstem and stay away from the tribs this time of year. A good place to start is the mouth of the Muddy River. I don't know if I would reccomend driving any great distance to fish the upper NF Lewis. From my experiences fishing can be a little slow there in September. I would suggest waiting a couple weeks and bring a float tube. Fish the upper NF in the morning and then fish Merrill Lake on the way back. From the end of September thru the middle of October is my favorite and my most successfull time to trout fish. Good Luck