Dr Joy said scientists were being bullied, and gave the example of an unnamed scientist who was asked to make a hydrological model in a certain way to support an irrigation project. The scientist refused, and pressure was put on him by his employer and by business.
He was to speak to Radio New Zealand about it, but the station feared being sued. Nothing has been said publicly so far.
In another example, the Ministry for the Environment said, in 2013, that freshwater quality in New Zealand was stable or improving. It used figures dating back 10 years to prove it. Dr Joy said 80 years' figures would have presented quite a different story.
He pointed that out, and was willing to talk about it with ministry officials on national radio. The officials would not front up. "They know that if they say nothing it will just blow over. Reporters can't force them to come along."
Dr Joy's Wanganui talk was titled Environmental Protection Failure - New Zealand Freshwater: A Case Study. Dairy farming came in for a lot of scrutiny.
One dairy cow excretes as much as 14 people. New Zealand's increasing cow numbers give the country an equivalent population of 90 million people.
The country's dairy industry used to be powered by sunshine and by clover adding nitrogen to the soil. Since the 1960s, countries worldwide have been using energy from natural gas to make the nitrogen present in the air into nitrogen fertiliser.
"We now create more than the whole planet does naturally, with most of it ending up polluting. Global use of artificially created nitrogen is six times higher than what the planet can handle."
Some Canterbury dairy farms leach 48kg of nitrogen through into freshwater per hectare. He said it costs 37 times as much to return that water to drinking water standard than it does to use less fertiliser. And the "grandparenting" approach allows farmers leaching the most nitrogen to continue.
"If you were a big polluter before, you get to pollute some more. It's rewarding the bad guys."
The push to produce more milk has also led to New Zealand being the world's biggest importer of palm kernel extract - at 2.3 million tonnes a year.
He's given up on Government doing anything to fix the situation, and is pinning his hopes on industry and a scheme to reward the most efficient producers.
For many dairy farms, reducing herd size by a third reduces costs, leaves them profitable and does way less damage to the environment.
In the industry scheme, the most efficient third of producers would be paid $1 more per kilo, and the bottom third $1 less, "to drive it in the right direction".
The Government's 2011 "National policy statement on freshwater management" contributed to his disillusionment. It set such low standards that it instantly made the state of most of New Zealand's freshwater acceptable.
The Yangtse and Mississippi, two of the world's most polluted rivers, would only fit into its middle band.
Rocks would be coated with algae and fish would be dying even in the best band, where most of the country's lowland rivers fit.
Insect health, temperature levels and oxygen content were not even in the criteria, and water had only to be suitable for wading and boating - not for swimming.
He painted a depressing picture overall.
Asked what an individual can do, Dr Joy had a surprising answer: "Take animals out of your diet".
"Five and a half billion people on the planet are supported by nitrogen made from fossil fuels. Animals have to go," he said.
-To check his facts, go to www.waterqualitynz.info.