Yep, it does go brown. If there are microscopic bugs in the troughs it should be okay. Its not the colour of the water, its what is living in it.
I sometimes used to chuck some green water in from our pond but not lately - my husband thought he was helping me by emptying a tank of 'rainwater' sitting on the outside table into our pond, instead he emptied a tank of tap water and bleach into it. The pond is sure clear now!!! :oops: