My workflow has been to load in the
.wav files I want to mix, and then start working, but it always had some low-level noise on the channels. Even when Ardour was not supposed to be playing, the noise would be there.
It turns out that Ardour still connects the inputs to the track, and passes them through the effects chain. This is why the noise responds to the fader, noise gate effects, and the like. The solution is to go to the input on each mixer strip and switch it from 1 (or 2, or 1/2, etc.) to "Disconnected" instead. Otherwise, at minimum, thermal noise gets added on the channel.
I happened to discover this through a pair of accidents: I had a cheap headset mic connected and noise was worse than ever, but also, all of the meters jumped when some background noise happened. Disconnecting the inputs fixed the noise, without affecting the ability to play back the imported audio.
(This isn't the normal fare for my blog, but if I put it on tumblr instead, it'll never be seen again, and what good is that?)