The nitrates in fertilizers get washed off the land as runoff into rivers, where they accumulate in bodies of water and foster algal blooms, which use up all the oxygen in the water and kill off or drive away everything else. This can get especially bad in coastal waters, where most of the rivers bringing the nitrates end up. Rivers can remove nitrates naturally, but not to the extent that they are being put into the river. And booms in crops like corn for biofuel only use more fertilizers, meaning that more nitrates will get into water systems and cause algal blooms.
This process of algae bloom is known as eutrophication.
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