"These issues are of particular concern when we consider the unique flora and fauna habitats in our fresh waters," University of Canterbury Professor Jon Harding said in a statement reported by China's official Xinhua news agency.
Water extraction from some river systems for irrigation has exceeded the total amount of water in the rivers, he said.
"Despite our dependence on this vital resource, we frequently take it for granted and heavily pollute and abuse it," he said.
"Many of our lowland streams, rivers and lakes are not clean. One of our largest lowland rivers, the Manawatu River, was recently described as one of the most polluted rivers in the world.
"Lake Ellesmere, or Te Waihora, is the largest lowland lake in New Zealand and it has been described as dead."
Harding, a freshwater biologist, will outline the severe damage to New Zealand's wetlands at a national conference on the Canterbury campus conducted by the Biology Educator's Association of New Zealand in July.