The US is a massive country friend, there are lots of places with combined sewers (domestic wastewater and stormwater) that will bypass treatment when there is a big rain event, especially in coastal cities that discharge wastewater to the ocean. It’s not ideal but the alternative is massively oversized treatment plants or replacing all of the existing sewer infrastructure to separate the sewers. Both options would cost tens of billions of dollars in any of the large east coast cities. People are not willing to pay for that.
As stated in the article, this isn’t a big problem for communities with centralized water treatment systems, rather for individual homes drinking well water which is contaminated by agriculture.
In a municipal treatment plant you have a few options for removing nitrates including reverse osmosis (membrane filters with very small pores, allowing them to reject very small molecules), ion exchange (swap nitrate with another, less harmful ion), or biological treatment (use microorganisms to turn nitrate into nitrogen gas).
In your home, reverse osmosis is really the only feasible option, which can be expensive to install and costly to maintain. Ideally, some sort of tax on fertilizer would be used to pay for these in house treatments, but that would increase the cost of food.