Electric companies often prefer to use cooling water from the ocean or a lake, river, or cooling pond instead of a cooling tower. This single pass or once-through cooling system can save the cost of a cooling tower and may have lower energy costs for pumping cooling water through the plant's heat exchangers. However, the waste heat can cause thermal pollution as the water is discharged. Power plants using natural bodies of water for cooling are designed with mechanisms such as fish screens, to limit intake of organisms into the cooling machinery. These screens are only partially effective and as a result billions of fish and other aquatic organisms are killed by power plants each year. For example, the cooling system at the Indian Point Energy Center in New York kills over a billion fish eggs and larvae annually.  A further environmental impact is that aquatic organisms which adapt to the warmer discharge water may be injured if the plant shuts down in cold weather.
Water consumption by power stations is a developing issue.
In recent years, recycled wastewater, or grey water, has been used in cooling towers. The Calpine Riverside and the Calpine Fox power stations in Wisconsin as well as the Calpine Mankato power station in Minnesota are among these facilities.