A long time ago, NL signed a couple of European agreements that forced them to designate a number of area's for which the natural diversity should be preserved. NL did this very diligently: no less than 162 of such area's were assigned. About 10 years after signing the contract, an environment organization started a lawsuit against a farm next to such an area that wanted to expand. It won the lawsuit and the farm's expansion was forbidden. The ground for the verdict was that the expansion would increase the farm's emission of nitrogen; a gas that when it ends up in the soil, favors a limited number of plants such as nettles and grass, most other species will die out.
Once this precedent was created, many more lawsuits followed. Eventually the Dutch government decided to make a plan to regulate nitrogen emissions nationally. A map was published that showed estimated levels of nitrogen emission in the country. In many area's the emissions were too high, and the most obvious way to bring it down was to close nearby farms. This is the reason for the farmer's protests.
Interestingly, very little is known about how much emitted nitrogen eventually ends up in the soil. The RIVM, the Dutch institution that made the map, only started doing some measurements of deposits in 2020. There's also a lot of criticism on the way the emissions are measured and on other aspects of the model that was used to create the nitrogen map.