Photosynthesis is interrupted. There have been reports of coral polyps feeding during the day in the cloudy water, something usually only observed at night. In addition, this sediment settles onto living coral tissue and may smother it. As with other threats of nature, there isn't a lot we can do to stop the impacts of wind on the reef. But there are things we can do to avoid compounding the problem.
Careful navigation is one way to protect the reef.
Diving or snorkeling when there is decent visibility is another common sense approach to lessening coral damage. Improving water quality is another way to ensure that, when the natural impacts are finished, the human-induced ones don't take over.