Putting the old media back is probably too late as it starts to die off in around an hour of being out of its normal environment.
If the water is brown then it is probably dirty and needs more water changes, if it is green then it is too much light, dissolved organics / Nitrate.
1) Follow the advice already seen in this email
2) Testl water parameters and report back Ammonia, PH, Nitrite and Nitrate.
3) Keep up some large water changes
If Green and Nitrates low then you could add a UV clarifier.
It does sound under filtered and it also sounds that the media is poor quality and not mature.