To pick up on the point about pond weed etc., I think that you don't get much of this on the Goyt because it is fast flowing. I also understand that the condition of the river is far better than it used to be and that we even have salmon jumping up the weirs (although I've not managed to spot them yet myself).
Regarding the smell, it may be worth reporting that to the Environment Agency. If they were concerned after you'd described it to them I think they would look into it further.