Waikato Regional Council measures water quality monthly at five sites from Mangaokewa to Whatawhata. The measurements show poor quality along most of the river, with excess nitrogen, silt and phosphorus, though E. coli levels have improved with improved sewage treatment, though generally not enough for safe swimming; recreational rivers should have median E. coli levels below 126 per 100ml, but Waipa's range from 160 to 320. Turbidity levels north of Otorohanga rise to more than double the levels needed to support plant photosynthesis and phosphorus levels also rise above targets in that stretch. Nitrogen levels increased at all five sites between 1993 and 2012 due to intensified land use, now adding 3,075 tonnes a year. By comparison, the total from sewage works and Te Awamutu dairy factory is 66 tonnes.