Why allowing nitrogen or phosphorus fertilization run into a body of water negatively effect life in it?

This is called eutrophication. The excess fertilizer causes overgrowth of water plants and they crowd the waterways. They cover the surface, the ones under the surface can not get sunlight and die. The rotting process uses oxygen. This uses up the oxygen needed for the other aquatic life. The BOD or biological oxygen demand is the problem. The decaying plantlife uses up all the oxygen and causes the fish and other animals to die. The rotting mess can get quite smelly.