The devastating floods that hit the top of the South Island in August also destroyed aquatic life in its rivers and estuaries.
Scientists believe 80 percent of the fish in Nelson's Maitai River are likely dead and say it'll take years for it to recover.
The Maitai River should be teeming with all sorts of life, but the August floods changed that.
"There's very little life - I'd expect a range of caddisflies, snails, perhaps some worms, mayflies," said Cawthron freshwater scientist Roger Young.
Those critters were stripped from their home when the meandering Maitai turned into a raging torrent. It left an almighty mess and killed at least 80 percent of the eels, trout, whitebait and other fish living in it.
"It was pretty devastating. There weren't many fish in the river for a while, and very little for them to eat," Young said.
The surviving aquatic life now has no shelter or shade, only piles of sediment, and hundreds of slips in the river's catchment run into it when it rains.
"After small rains it gets dirty quite quickly. Thinking about the health of the river, it's something that will affect this river for a few years, maybe longer."
It's not just the region's rivers but its estuaries and ocean too. Satellite images from before and after the flood show huge sediment plumes.
Cawthron marine biophysical scientist Ben Knight said the difference from after the August flood and slips is massive.
"A lot of that sediment has gone into Tasman Bay and Golden Bay," he said.
"This is having an impact on the bays. I know there are a lot of scientists around New Zealand working on the problem and looking at reducing our impacts."
An impact that's really being felt in areas like Nelson's Haven Estuary, where seagrass beds have shrunk because of sediment from flooding and slips.
"Seagrass beds and mud in general trapped a lot of it here, so we experienced a lot of burial of seagrass and as a byproduct of that we are seeing biomass loss. The coverage of seagrass is declining," Cawthron marine ecologist Emily McGrath said.
Bad news because seagrass is critical to the survival of many marine species and a refuge for young fish.
"If these beds are reduced then you could expect adults to suffer, because numbers are going to decrease in that population," McGrath said.
"Seagrass beds also act as a carbon sink, so they have the ability to absorb CO2 which is incredibly important in the changing climate crisis."
But amid this crisis there's also a glimmer of hope. Young has seen new life emerging in the Maitai River - signs the ecosystem is fighting back and its recovery is already underway.
