A couple of years ago Lindavia Intermedia, a slime known as lake snow, was found for the first time in the Waikato and there is no known way of removing it.
Darion warns that some freshwater pests are microscopic and can spread with just a single drop of water.
"Even if you can't see the pest, you could still be spreading it," says Darion.
Hunters should 'Check, clean and dry' any equipment that has come into contact with river or lake water.
"We are asking hunters moving between waterways to 'Check, Clean, Dry' any equipment that has come into contact with river or lake water – particularly boots, decoys, boats and boat trailers," Mr Embling says.
All items, particularly boots, decoys, boats and boat trailers, should be checked and any debris found needs to be left at the waterway. All items should be cleaned for at least a minute and using a five per cent biodegradable dishwashing solution. Water absorbent materials such as boots require longer soaking times to allow for thorough saturation.
And lastly, all items need to be completely dried to touch inside and out and then left to dry for at least another 48 hours. This is to ensure all cells are dead. Even slightly moist items can harbour microscopic pests for months.
Boat safety is also important for people heading out onto the region's waterways.
"With this type of cooler weather we know hunters will typically be wearing gumboots, heavy clothing and carrying ammo, and more often they'll be getting into small boats to travel to their maimais," says Waikato Regional Council's maritime services team leader Richard Barnett.
"That makes them really vulnerable if the unexpected happens and they end up in the water, even though the water in some places might not be very deep.
"Our council's navigation safety bylaw is really clear. If you're in a boat under six metres and it's under way, every person on board must be wearing a properly fitting lifejacket – no matter what waterway you're on in the Waikato."
Mr Barnett says it is also important to check your boat is in good condition before heading out.
"This involves making sure lifejackets are in good order and there's enough for everyone on the boat. Make sure your boat's in good shape by looking at everything from the outboard to the fuel and filters, the batteries and navigation lights," he says.