The deterioration of water quality would be most pronounced in Canterbury and Southland.
"The outcome of the modelling exercise is not good news. I had hoped it would be otherwise. It is almost inevitable that without significantly more intervention, we will continue to see an on-going deterioration in water quality in many catchments across the country."
Dr Wright said much effort and investment was being made to protect iconic lakes, mitigate pollutants and find innovations to protect waterways.
Despite these changes and the expansion of forestry, the amount of nitrogen entering fresh water was projected to increase in every region of the country except Gisborne.
She said the type of catchment was important to how polluted it became. On the West Coast, nitrate levels were very high but the water quality was not affected because the nitrogen was carried quickly out to sea.
The report said New Zealanders faced a difficult dilemma because the dairy sector was now the biggest earner of export dollars.
"In much of my work, I actively seek out 'win-wins' for the economy and the environment. But in this case, New Zealand does face a classic economy versus environment dilemma."
She said the Government's freshwater reforms were a positive step. But the goal of maintaining or improving water quality in all regions would not be reached unless policy makers more actively addressed the connection between changing land use and water quality.