The Department of Conservation (DoC) had erected signs near the site, warning track users of potential contamination.
On Saturday morning, council staff confirmed the discharge point of the sediment as an old mining asset above a stream opposite the Karangahake Gorge carpark.
Council investigators and scientists were returning to the mine entrance again on Monday.
Water flowing from the mine on Saturday was running relatively clear, while there was still visible sediment which had settled in the stream and river in quiet locations or around rocks.
The council said there was heavy rain forecast this week and a lot of water was expected to flow from the surrounding hills into the Ōhinemuri River, which might trigger more flushing of the settled sediment down the stream and into the river.
People could expect to see more discolouration until all the sediment had been flushed out of the stream.
Lynch said council staff would now complete a thorough scene examination, including how the event occurred and what a “normal” discharge from the mine should look like.