In Taranaki, the plant was first discovered in a lake in 2012, and again found last summer at Lake Herengawe, locally known as Lupton's Lake, a popular boating spot near Waverley.
In recent weeks, council officers doing routine lake monitoring spotted it in a third lake, Lake Mangawhio, about 30km northeast of Waverley.
The plant is notorious for becoming caught on boats, kayaks, fishing gear, eel nets and duck shooting equipment, allowing it to spread so easily between bodies of water.
Council environment services manager Steve Ellis said hornwort could have disastrous effects on the region's environment if it spread further around Taranaki.
"It just takes one fragment the size of a fingernail to cause a new infestation. If people are not vigilant in cleaning their gear it will inevitably spread and then we're fighting a losing battle.
"Once a weed such as hornwort becomes established in a lake or waterway the cost and logistics make it almost impossible to eradicate. That's why our focus has to be on prevention."
Ellis said the council was working closely with South Taranaki iwi Ngaa Rauru to raise awareness and educate the community about the damage hornwort and other aquatic pests could do.
The council was also working with the Ministry for Primary Industries, Department of Conservation and Land Information New Zealand around the recent discovery.
"We want you to get out and enjoy summer in and on our lakes, whether in Taranaki or further afield. Just remember to 'check, clean, dry' when moving between waterways.
"It's a simple, quick thing we can all do to protect our unique biodiversity and stop the spread of pests."