Farmers still have a long way to go to meet some water clean-up targets, but the work done so far should be acknowledged, Dairy NZ says.
The organisation has published its three-year report of the industry's Water Accord, which involves 11,400 farmers undertaking work on their farms to protect freshwater.
However, Otago University professor of freshwater ecology, Gerry Closs, said the moves the dairy industry had made to clean up waterways should have been in place much earlier.
"The industry claimed years ago that everything was right, but when you see what they've had to do, it certainly adds weight to the argument that we were lagging when it comes to environmental protection."
Some of the headline achievements Dairy NZ was keen to promote after three years of the Water Accord include 97 percent of dairy cattle now fenced off from waterways on farms.
And 99 percent of regular stock crossing points on dairy farms now have bridges or culverts to protect local water quality.
However, the farmers have fallen short on having a riparian management plan in place.
The aim was to have a plan in place in half of the dairy farms by May last year, but only 27 percent of farms have done this.
Dairy NZ chief executive, Tim Mackle, said the farmers did have a lot to achieve, and it could be down to economic pressures that some of it had not happened.
In the last two decades, dairy cow numbers have rapidly increased. For example, in Canterbury they are up 490 percent to 1.2 million, and in Southland the numbers have risen 529 percent to 730,000.
Nitrogen leaching from agricultural soils increased by 30 percent between 1990 and 2012.
There has been a focus on farms to manage this, and the accord had a target to collect nutrient management data from 85 percent of dairy farms back in 2014, but three years later and it has still not been achieved.
Professor Closs said the country was moving into uncharted territory when it came to nitrogen loss.
"It can take many decades to recover the situation should things go wrong and nutrients get into groundwater in significant amounts, which is actually happening.
"There are areas of groundwater which are getting quite significantly enriched. And that will be a problem for potentially decades."
Dr Mackle said nitrogen reporting was difficult and challenging at the start, but there had been a change of attitude from the farmers.
"Starting out, it was really about education and getting people in the right space to be able to then start to manage these impacts down the track and that's where we are heading to now. We'll keep working on that one. We know we're not quite there yet."
Veterinarian and ecologist, Alison Dewes, said the nitrogen reporting was very confusing and farmers needed and wanted better leadership on the matter from their industry, including Dairy NZ and Fonterra.
That leadership also needed to acknowledge that fencing stock out of streams was not going to fix the long-term legacy problems with nitrogen and pathogens, she said.
"The public are really upset about swimmability. Our kaimoana down the coast is not safe for eating in many cases. We've got to start looking at real solutions and not just stock exclusion.
"We are going to need wetlands. We are going to change to farm systems. We are going to need to take heavy, intensive land uses off vulnerable soils."
Wetlands are often described as the kidneys of the land - they filter nutrients and sediment from water and are important habitats.
This is another area where the accord failed to meet its target of 100 percent of stock exclusion of all wetlands by 2014.