The Marlborough District Council says it is managing sewage overflow by pumping excess wastewater into flooded rivers.
Blenheim's sewerage system was overflowing on Sunday, following heavy rain overnight.
The council's three waters engineer, Stephen Rooney, said the controlled pumping would contaminate the rivers short-term but it was better than leaving the sewage to overflow onto people's properties.
"The alternative of the managed overflow is much more palatable, if you like, than having it flow around people's households."
He said the system should be back to normal by late this afternoon.
Rooney said this was Blenheim's worst sewerage problem since the system was damaged by the 2016 Kaikōura earthquake.
While the bulk of pipes badly-damaged in the earthquake had been repaired, he said minor cracks or slight joint failures in others could be contributing to the problem.