Generally speaking, noise pollution affects animals by reducing the area of usable natural habitat. Areas which are noise polluted cannot be used by animals. In some cases, whales have beached themselves in response to the military’s use of low frequency active sonar.
“Noise pollution” is a somewhat loaded term meaning noise that people find annoying or that is outside of some legal limit.
The question more specifically could be: “What effect does human-made noise have on animals?” In most cases it’s unuseful to animals, because human-made noises generally don’t represent any threat or communication to them, and get in the way of hearing sounds that are threats or communication.
But there are a lot of variations on this theme. As gitwithrico noted, the huge, powerful amount of ocean noise generated by naval vessels is probably responsible for killing whales. It’s been observed that city-dwelling birds change their song so they can be heard above the prevailing noise. On the other hand, humans make some noises that animals are very much interested in hearing: Like the call to feeding time. Some animals — even including wild animals — enjoy music at moderate levels.
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