This can affect bird and fish feeding. To avoid this, operate your PWC in deeper water. If you do have to traverse shallow water, run at idle speed. In coastal areas be aware of low tide. Low water levels expose sea grass beds and other delicate vegetation.
Disturbances can cause erosion and long lasting damage.
As a side effect, ingesting seaweed and seagrass is not good for your engine. Feed it clean water and it will run and maneuver much better. A PWC near shore can interrupt feeding and nesting wildlife, and cause animals to deviate from their normal behavior. And that, by law, is illegal. Mammals such as otters, manatees, and whales can be injured by direct contact with a boat, and it is believed that the noise from watercraft can even adversely influence breeding cycles and cause birth defects.