He will tomorrow outline some of his findings to the Australian Agricultural and Resource Economics Society's annual conference, being held in Rotorua this week.
In trying to clean up streams, lakes and rivers, the country was already burdened with a legacy of historic land use that, in some cases, could mean nitrogen would not show up in lakes for 200 years.
"It may get worse before it gets better, but in the long run, we will be better off because of contaminant limits."
Dr Doole believed greater restrictions on contaminants into waterways - which also included phosphorus, E.coli and sediment - would see the industry become sustainable but render some farms uneconomic.
"In the future, there will always be contaminant loss, but it's about balancing - how clean do we want our waterways?
"Because if we want them like they were 200 years ago, we might not have any agricultural industry left."
Easing stocking rates, as Federated Farmers has previously suggested, would only solve part of the problem, he said.
But he was heartened that the Government, industry leaders and scientists were together looking for solutions.
The issue is one of the greatest challenges facing the dairy industry, which would have to lift its exports by $14 billion to meet the Government's 2025 growth target, yet is already blamed for the worsening state of fresh waterways.
According to the most recent report from the Ministry for the Environment, around two thirds of monitored sites were unsafe for swimming.
A 2013 report by the Parliamentary Commissioner for the Environment, Dr Jan Wright, also painted a grim picture for New Zealand's lakes, rivers and streams.
The conversion of low-intensity sheep and beef farming to dairying had led to increased leaching of nitrogen and phosphorous into waterways, which spurred the growth of weeds and algae, and worsened quality.
By 2020, it was predicted 400,000ha of land would have been converted into dairy farms in the preceding 12 years - and even under optimistic assumptions, the report said, leaching would continue to increase.
Massey University freshwater ecologist Dr Mike Joy was much less optimistic about the future of our waterways.
Dr Joy agreed with Dr Doole that the situation would become worse before it got better, "but we don't have 100 years - we need have it coming right, right now - so we need to do something drastic right now".
He called for widespread improvements in farming systems and management - and a tougher stance on contaminant levels.
"The National Objectives Framework in the latest National Policy Statement is a complete back-down on the limits - we've gone from a limit of 0.5mg of nitrogen [per litre of water] to a nitrogen limit of 6.9mg," he said.
"It's like a 50km/h speed limit going to a 690km/h speed limit, and then saying you are going to improve road safety."
