Whatawhata was a Ngāti Māhanga village and there are still Te Papa-o-Rotu and Omaero maraes on the west bank of the river. In early colonial times Whatawhata was one of many sites in Waikato with a flour mill. It was built in 1855 and producing flour by the end of that year. The area must have been suited to wheat, for there was another mill about downstream, at Karakariki, by 1860.
European settlement
British troops arrived at Whatawhata over land and by river, as part of the Invasion of the Waikato, on 28 December 1863. Whatawhata was described as having no end of peach trees, which the soldiers stripped of their fruit. Within a year a telegraph line had been built. A 1915 guide described Whatawhata as, "six miles from Frankton Junction, along a good metalled road. Coaches run to and from Frankton Junction daily, the fares being 2/- single and 3/6 return. The principal industries are farming and dairying. There is one hotel in the township, also school, and post and telegraph office. Small steamers ply up and down the river from Huntly, the waters being navigable as far up as Pirongia. Whatawhata was in the early days an important Maori centre, having at one time a native population of over a thousand." Since then the post office has been replaced by a petrol station and dairy, the coach has become 4 per day and the river is rarely disturbed by any craft. Also the AgResearch hill-country research station at Whatawhata was started in 1949. Across the road from AgResearch, Campbell Coal Ltd developed a coal mine in 1920, was advertising for about 10 tons a day to be carried to Hamilton in 1921 and had it fully open by 1923. It produced 9,272 tons in 1945 from a seam, employing 6 miners and 5 surface workers. Hallyburton Johnstone said there was never a strike at the mine. The coal was sub-bituminous with a fairly high calorific value, but was largely worked out by the 1970s, when Hamilton gasworks closed. 2.9m tons is estimated to be still recoverable. An 1880 guide said, "It is about ten miles distant from Hamilton, but a sum of money has been voted for making a direct road through a large swamp, which will bring the Hamilton station within six miles of the township. The road to Raglan crosses the, Waipa river here, and a bridge will shortly be built, when the ferry, which is now worked by natives, will be done away with. Heavy goods, such as timber, wire and manure, are brought up by the Waikato Steam Navigation Company's steamers... There is a convenient school in the township, where there is an average attendance of nearly forty children. The school-house and teacher's residence, erected a short time ago by the Board of Education, the settlers contributing largely towards them, are excellent buildings... two stores, a bakery, and comfortable hotel. Of this last Mr. G. T. M. Kellow is proprietor. He has good accommodation and stabling, and keeps excellent liquors... Mr,W. H. Bailey has a general store and bakery... convenient to the Raglan and Whatawhata bridge site... Mr. Day has a farm| of 1,000 acres... five acres in oats and the same in mangold... wheat thirty acres... a large dairy... pigs... trees are kahikatea and rimu, with a little matai... Whatawhata racecourse... runs right round the township" A post office opened in 1868, burnt down in 1913 and was rebuilt in 1915.
The 2018 census used different boundaries, with a 2018 population of 2,763 in Whatawhata East, up from 2,214 in 2013. Whatawhata's village area had a 2018 population of 303, up from 273 in 2013.
Education
Whatawhata School is a co-educational state primary school for Year 1 to 8 students, with a roll of as of.
