The regional council released a report last week showing the river's entire catchment was polluted as levels for bacteria, sediment and nutrients measured over seven months were well above accepted levels.
Council environmental information and science director John Threlfall said the water-quality samples were taken in the upper reaches of the east and west branches of the Tokomairiro River - well above where Milton's wastewater treatment plant discharged into the river.
The site closest to the plant, the mainstem at Tokoiti, recorded a median E. coli concentration of 900 faecal coliforms (cfu) per 100ml of water.
"The water is highly compromised above that."
Tests upstream in the Moneymore area, also above the discharge point, had the highest E.
coli counts, a median concentration of 1100cfu per 100ml.
The contact recreation standard for E. coli in waterways is 126cfu per 100ml of water.
The report showed E. coli counts for low flow samples in the west branch of the river were unusually as high in the top of the catchment as they were lower in the catchment.
"In previous intensive catchment investigations, E. coli counts are generally very low at the top monitoring site compared to the lower monitoring site."
The median concentration for the west branch at SH8 was E. coli at 490cfu per 100ml water, and at the east branch at SH1 it was 1400cfu per 100ml of water.
It was not known what caused the high E. coli counts at the top site but it was "likely due to local agricultural inputs which are then diluted further downstream", the report said.
Mr Threlfall said while there had been issues with discharge from the wastewater plant in the past, it had been upgraded and was operating within its consent.
The standards it had to comply with were lower than normal because of the poor state of the water above its discharge point.
Once the water quality was improved upstream from the discharge point, the council could look at stricter discharge standards for the plant, he said.
