The Paedosphere Connection

For Dairy farms to be economically viable, farmers seek to obtain the best return in the most cost efficient way. In order to increase productivity on farmland and increase postural growth, fertilizers are applied to the exposed surface in order to promote such growth. As has been discussed, these fertilizers contain ammonia, which through nitrification eventuates into becoming Nitrates. Since the 1930’s and even preceding this, vast swathes of natural vegetation was cleared from land in the Waikato region, including in marginal area along the banks of waterways for allow for the development of cities, towns, and agricultural pastures. This, accompanied by the increased intensification of the land has degraded the quality of the soil within the region. The quality of which can be viewed on the Waikato Regional Councils interactive soil quality map found here: 

http://giswrcmaps.waikatoregion.govt.nz/wrcmaps/framesetup.asp

So how is soils contributing to the issue of Nitrates entering the Waikato water-ways, eventually leading to it's overall declining quality? Simple, it's providing a source of conversion for fertilizers to chemically change from Ammonia into Nitrate, and then being redeposited by dairy cows urinating in concentrated sections where it can leach through into the groundwater table, or runoff into streams and rivers. A simple explanation (inclusive with visual guides!) by farming commentator Glen Herud: 

Glen Herud - An explanation on Nitrate leaching through soils. Source: Youtube.

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Sources: 

Waikato Regional Council - http://www.waikatoregion.govt.nz/

Glen Herud explanation - https://www.youtube.com/watch?v=Rrte1-mHXGo