The fragile ecosystems in five provinces were ripped apart by the same storm that killed an estimated 10,000 people in Central America.
"We lost biological and cultural riches [and] medicine," said the Humboldt Centre, a non-government organisation sponsored by German and British environmental groups.
It added that some communities had lost food supplies, and in some areas, the hurricane damage was irreversible.
"Wildlife, especially iguanas, were seriously impacted by the destruction of the habitat that serves for refuge, food and reproduction," the group said.
The hardest-hit areas were the basins of the Coco and Matagalpa rivers and the Lagoon of Managua.
The rainfall from Hurricane Mitch was 15 times heavier than normal, eroding hillsides and stripping leaves from trees. The rushing water also spread pesticides and poisonous chemicals from gold mines over wide areas, the centre said. The chemicals affected the mangrove swamps and great numbers of sea creatures, especially shrimp, were expected to die in the coming weeks.
The disappearance of some species will also allow the invasion of other, harmful, types such as rats and insects that could spread disease.
The Humboldt Centre appealed for international aid to try to save what was left but said it will take at least 35 years to recover some of the affected areas.
For now, relief efforts on the Coco River are concentrated on saving the native Miskito communities. About 40,000 Miskitos lost their harvests and 80 per cent saw their homes destroyed, Congressman Steadman Fagoth told a Mexican government news agency.
British ships and helicopters have tried to bring food to hamlets and rescue villagers stranded by waters that rose 50 feet.Reuse content