Boats are more likely to hit the reef when they are struggling against wind. Diver and snorkelers, if they can get out to the reef, are more likely to accidentally touch coral if the visibility is poor, and more likely to stand on it or bump against it if they are struggling with waves. But probably the most severe impact of a windy season is something as innocuous as cloudy water. Sediment suspended in the water column doesn't get a chance to settle. Without sunlight, the natural symbiosis between the coral and its algae partner are thrown out of whack.
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.