As part of the project teams of farmers, conservationists, local authorities and iwi will develop action plans for each water body.
"Today's announcement is about investing time and resources to improve their quality so that we can all enjoy our natural environment at its best and ensure this can occur alongside a sustainable dairy industry," said Fonterra director John Monaghan.
But the agreement put DoC's responsibilities to protect nature at risk, said Green Party conservation spokeswoman Eugenie Sage.
Government funding cuts of $54m had forced the organisation to rely on corporate backing, which was taking focus away from its key priorities that is instead being steered into projects businesses want, said Ms Sage.
"DoC is being put in a situation where it is reliant on funding from a company that it has to hold to account.
"If Fonterra really wanted to do something for the environment it could work to restrain the growth of intensive dairying and stop dairy expansion in sensitive catchments like the Mackenzie Basin and Southland's Waituna Lagoon,'' she said.''