More than 3500 birds and hundreds of eels have been found dead in waterways on the Hauraki Plains in the Coromandel.
Scientists and conservationists say the crisis is the worst they've seen in decades, and it's putting two areas at risk that are regarded as internationally significant.
Fish and Game officers are in a state of disbelief as they document the death and decay in the Piako River.
"It's definitely one of the worst environmental issues or disasters that we've seen up in that area in my working history anyway," Fish and Game Auckland-Waikato manager David Klee says.
Eels trying to flee waters are choked by algae, which reduces oxygen, and they have ended up suffocating in drains blocked by floodgates.
"Those are all eels, there are a few goldfish. We've already picked up the dead duck out of there," says Mike from Fish and Game.
Ducks - as well as protected species like shags, banded dotterel and herons - have succumbed after a botulism outbreak which is exacerbated by the dry conditions.
The crisis in the Hauraki Plains is being created by several issues. Record low flows in rivers due to drought conditions has allowed algae to flourish. Adding to that is the increased nutrient runoff from factories and farms.
Freshwater ecology senior researcher at Victoria University Dr Mike Joy says New Zealand has a "shocking record" when it comes to freshwater fish.
"We have three-quarters of our freshwater fish on the threatened species list, and that's a higher proportion than I can find for any other country in the world."
The Piako River connects the Kopuatai Peat Wetland and the Firth of Thames mudflats. Both are considered internationally important because they're home to numerous species of birds.
Klee says we're at risk of losing these internationally significant sites.
"I think in the long term if we don't start changing the way we treat these resources then there is a risk, yes."
The Waikato Regional Council acknowledges it needs to ramp up efforts to protect the environment.
"We would always say we need to do better, we need to do more," the council's science manager Dr Mike Scarsbrook says.
He says stricter rules on developments are coming, and they are looking at projects to improve drainage and passageways for fish so they can escape to better water.
"These eels are our native species. There's no difference between the value of these eels and the value of kiwi and kakapo."
Joy believes not enough is being done to help freshwater fish survive.
"What we're seeing around the whole country is the failure of government - local and central - to do anything about the impacts on freshwater in NZ."
He says this will only get worse unless we take action to reign in our decades-old exploitation of these and other waterways.