At Ōtorohanga, the Primary School and surrounding houses were flooded, when the river spilled into its old course (see map below) and filled the area behind the stop banks.

[18] Work was done in 2006,[19] but, in 2007, Hydro Energy ( Waipā) Ltd was fined for unconsented damage to native vegetation in building the penstock.

[22] In 2017 Nova Energy gained consent[23] to build a 360MW gas-turbine station (connected to the Maui Gas Pipeline) on the Ongaruhe Stream, close to its confluence with the Waipā.

[24] The mid-merit Waikato Power Plant at 869 Kawhia Rd, Ōtorohanga was expected to be used for 10 to 15 minutes, 3 or 4 times a day,[25] but was shelved in 2021.

[27] 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;[28] recreational rivers should have median E. coli levels below 126 per 100ml, but Waipā's range from 160 to 320.

[33] Ministry for the Environment figures[34] averaged between 1998 and 2007 showed the Waipā at Ōtorohanga had 280 E.coli per 100ml (53rd worst out of 154), 360 faecal coliforms per 100ml (83rd of 252), 0.55 mg/litre nitrogen (161th of 342) and 0.03 mg/litre phosphorus (187th of 361).

Pollution has been worsening for nitrogen and phosphorus, though turbidity has improved, as shown in this table of important (ie slope direction probability over 95% and RSKSE over ±1% pa) improvements, or deteriorations (-) in relative seasonal Kendall slope estimator (RSKSE) trends (% per year).

Regional Council estimates that 8,718 ha (21,540 acres) is at risk of severe erosion in the Middle Waipā (Waitomo, Turitea, Pirongia, Karakariki, Puniu, Mangaotama, Mangawhero and Mangapiko catchments) and 350 km (220 mi) of stream bank to be prone to erosion.

[37] Listed in order from the confluence with the Waikato and moving south they are:- Over 50 kilometres (31 mi) was navigable by waka and Pirongia (Alexandra) was busy as the head of steamboat navigation until the railway was built to Te Awamutu in 1880,[43] though some settlers used it as far as Te Kūiti,[62] though possibly only as far as the confluence of the Mangapu and Mangaokewa streams, about 4 mi (6.4 km) upstream from Ōtorohanga.

[72] An 1881 article said a journey upriver would normally take 36 hours, but more in dry weather, when shoals at Whatawhata and Te Rore were hard to cross.

[74] Around 1900 the Freetrader, owned by the Waikato Company, "was withdrawn owing to competition from the Walsh brothers with their launch Victory, which could traverse the winding Waipā much more easily than the cumbersome stern-wheeler.