Now, this farmer claimed that the nitrate content we see now is decades old, that the bylaws and controls as well as agricultural practices in place now work. Is this true? Does nitrate penetrate ground so slowly? The only mechanism here I could think of that nitrate is adsorbed and desorbed on minerals in the ground, sort of like in chromotography column.

If neccessary, I can provide more figures for nitrate content of specific wells, groundwater table etc - but I don't think it's neccessary since I want a qualitative answer wether or not such a slow infiltration is plausible at all.

The situation with fertilizer and urine is much more complicated, however, because there are multiple nitrogen species and transformations that occur in the nitrogen cycle. Nitrogen fertilizer may be applied in a number of forms including urea, ammonia, nitrate, or mixtures of these. Urea is commonly used in my area, anyway, because of its low cost.

Urea is converted to ammonium in the soil. Urea and ammonium are cations and strongly sorbed to soil particles. Ammonium can be volatilized and lost as gaseous ammonia but is also transformed to nitrate by nitrification.

Nitrate is the main form of nitrogen that is assimilated by plants. It can also be transformed to nitrogen gas by denitrifying bactera. Some plants such as pulses (e.g. peas and beans) have a symbiotic relationship with bacteria in their root nodules that fix nitrogen in soil gas to ammonium, which is then used converted to nitrate by nitrification and used by the plants. Nitrogen is also released to soil by decomposing plant matter.

There are other nitrogen species, but they tend to be transient products along the chain of reactions described above.

So the farmer is partially correct, much of the nitrogen in the soil is in a form that is not readily available for uptake by plants or by leaching to groundwater. But is incorrect to say that current impacts are only due to old nitrogen and that the problem has been solved. As long as nitrogen is being added in one of the various forms, the transformations are ongoing, nitrate is being produced, and this nitrate has the potential to pollute groundwater. Note, also that ammonium and nitrate can be transported through surface water, either sorbed to sediments or dissolved, which can be an even bigger pollution issue.

Here is a link to a video on nitrogen transformations in agricultural soils and to notes on the video, for those that prefer to read.