Patrick Boyle, a Water Security Agency spokesman, says charges were laid after an inspection of the treatment plant last July.
The city didn't keep and provide records of turbidity — how much cloudiness there is in the water — and didn't do required water quality monitoring for some constituents.
But Boyle says regular monitoring for bacteria was done and the water was always safe for people to drink.
He says the issue was one of record-keeping and there was no failure of the water filtration system.
Thousands of North Battleford residents became sick in 2001 when a parasite called cryptosporidium entered the water supply during routine maintenance of a chemical filter.
"An audit has been done internally to investigate any other irregularities. None have been determined," North Battleford Mayor Ian Hamilton said Friday.
"Going forward, we have put in internal controls ... to ensure that we are always compliant with our testing and our reporting to the ministry."
— With files from CJNB