Freshwater scientists say boaties have inadvertently damaged more than 90% of the country's most accessible lakes which are now polluted - some choked - with invasive plants.
Experts from the National Institute of Water and Atmospheric Research (NIWA) have relaunched a website rating the country's lakes.
The site, http://lakespi.niwa.co.nz, gives 250 of the country's lakes a score reflecting how damaged they are by such pollution.
NIWA head of freshwater biosecurity Dr John Clayton says much of the harm is caused by boats and trailers picking up vegetation and accidentally transporting it to lakes.
Dr Clayton says once the invasive plants take hold they can end up causing problems for boaties and swimmers who can become entangled in them.
There have been cases of people drowning in dense weed beds.
From an economic point of view, Dr Clayton says, irrigation systems can be affected and hydro power stations can lose millions of dollars worth of electricity generation a year due to weeds clogging intake screens.