The natural Whangamarino River system, especially the main branch (the southern catchment), has been highly modified due to the lower flood protection scheme of the lower Waikato River.

[1] Prior to these floodworks, the Whangamarino Catchment was unconnected with Lake Waikare.

While the flood scheme has permanently changed the ecology of Lake Waikare, it has also provided broader benefits for the community.

[2][3] The Whangamarino River includes the large Whangamarino Wetland (5,193 hectares) which is the second largest bog and swamp wetland in the North Island of New Zealand (after the Kopuatai Peat Dome).

The wetland includes peat bog, swampland, mesotrophic lags, and open water river systems are managed as both Wetland and Wildlife Management reserves by the Department of Conservation.