Boat operators should remember that water pollution ruins not only the aesthetic beauty of the area, but harms human life, marine life and damages boating equipment. The degree and amount of garbage adrift on our coastal waterways continues to increase. Plastic, which many species mistake as food, is a big threat to marine life. Birds are found entangled in plastic rings, fishing line, or nets. Various federal and state laws prohibit throwing, discharging or depositing any sort of refuse matter in the waters of the U.S. Other acts require boats of various sizes to display placards and keep records of their refuse disposal. A person who violates any of the requirements is liable to civil penalties, fines, and imprisonment. Regional, state, and local laws may also have specific restrictions on refuse disposal.

The spread of aquatic nuisance species (ANS) by recreational boaters is an increasing concern across the country. Milfoil, zebra mussels, quagga mussels and other ANS are being increasingly regulated by states to prevent their spread, with specific regional, state and local laws.