The region includes flat floodplains, rolling hills, mountain ranges and steep volcanoes. It has 100 lakes, 20 rivers and 1420 streams, as well as three internationally important wetlands: the Firth of Thames, Kopuatai Peat Dome and Whangamarino.
The Waikato has warm, humid summers and mild winters. Rainfall varies considerably across the region, with an overall annual average value of about 1250 mm. This is generally considered adequate for agricultural production, although there is potential for drought in summer.
Air quality in the Waikato region is generally good but because most of the main urban centres are located well inland where cold, calm conditions can occur during winter, this can lead to high concentrations of fine particulate matter, mainly due to solid fuel burners and open fires.
Pastoral farming covers more than half of the land, and indigenous vegetation and plantation forestry are also important land uses, covering about 28% and 12% of the region's area respectively.