Water Quality

aerial view of a boat in clear, turquoise water over a coral reef.
The water color in the Florida Keys varies depending on the depth, what's on the seafloor, wind conditions, and other factors. On a clear day, the water may be sparkling shades of blue and turquoise. Photo: Jack Fishman

Good water quality is essential to a healthy marine ecosystem. Seagrass and coral reef habitats thrive in clean water that is relatively low in nutrients. When too many nutrients, sediment, and other pollutants such as metals, oils, and pesticides enter the water, they smother coral reefs, speed the growth of damaging algae, and lower water quality. Pollution can also make corals more susceptible to disease, impede coral growth and reproduction, and cause changes in food structures on the reef.

In the Florida Keys, our expansive watershed includes all of the rivers and streams that drain into Florida Bay, the Southwest Florida Shelf, the Gulf of Mexico, the Florida Straits, and the Atlantic Ocean. This means that pollutants from as far away as the Mississippi Basin, or as close as your own backyard, can enter the system and reduce water quality. These land-based sources of pollution can disturb how the ecosystem functions and impede coral growth and reproduction.

a watershed made of lakes, rivers, groundwater, and an ocean, with grassy areas, a beach, agriculture, roads, houses, a city, and more. The text explains the land-based sources of pollution that comes from each.
Infographic: NOAA

For more information, read the Water Quality Monitoring Program Science Summary.

How You Can Help

Within Florida Keys National Marine Sanctuary, recommendations for actions to restore and maintain water quality conditions needed to sustain healthy plant and animal populations are generated through the Water Quality Protection Program. Thankfully, there are also simple things that you can do to reduce the amount of pollution that eventually makes it to Florida Keys waters.

Plastic bottles wedged into rocks along the seashore
Marine debris, such as plastic bottles, are a hazard to marine life and the environment. Photo: Scott Atwell/NOAA

Refuse, Reduce, Recycle, and Reuse

  • Refuse non-essential single-use plastics. Choose reusable items like bags and water bottles instead of their single-use counterparts.
  • Dispose of your trash properly. Trash degrades water quality and harms birds, sea turtles, and other marine life.
  • Recycle as many materials as possible to keep from adding unnecessary solid wastes to land-fills. In the Florida Keys and most communities with single-stream recycling, the following items are accepted in recycle bins: rinsed glass bottles and jars, rinsed aluminum/metal cans, cardboard, regular paper, magazines, newspapers, junk mail, boxboard, rinsed milk and juice cartons, clean aluminum foil and any plastics marked with #1 through #7 (no plastic bags, blue glass, or Styrofoam).

Pesticides and Fertilizers

  • Follow label instructions for the use, storage, and disposal of pesticides and fertilizers if you use them. Dispose of these chemicals with other hazardous wastes. Insecticides are harmful because they can affect the nervous systems of aquatic animals. Fertilizers contain nutrients, which can fuel algae blooms that cause low dissolved oxygen, cloudy water, and other undesirable conditions.
  • Avoid using pesticides and fertilizers prior to a rain shower and take other steps to reduce runoff from land. Keep pet wastes and lawn clippings from entering any waterways, including canals and nearshore waters. If you live on the water or near waterways, create a barrier or berm in your yard along the waterfront to reduce runoff from your property.

Prescription Drugs and Medicines

  • Do not put prescription drugs or medicines down household drains or flush them down toilets or marine heads. Instead, drop them off at a facility provided in your community. These substances can interfere with growth and reproduction in aquatic animals and should be kept out of marine waters. Check with your local law enforcement office for drop-off programs and locations.

Detergents and Cleaning Products

  • Use non-toxic, biodegradable, phosphate-free products when cleaning your home, boat or car. Detergents may contain phosphorus and harsh chemicals that degrade water quality. The U.S. Environmental Protection Agency certifies cleaning products that meet EPA Safer Choice standards.
  • Do not pour cleaning solvents and other hazardous wastes down drains, marine heads or toilets. Instead, dispose of them properly with other hazardous wastes.
Two boats that are partially underwater and laying sideways in shallow water
Inoperable vessels anchored nearshore invariably become derelict wrecks following storms. Photo: Scott Atwell/NOAA

Vessel Sewage/MSDs

  • Marine sanitation devices (MSDs) must be locked and in the closed position while in sanctuary waters.
  • Discharging vessel sewage, treated or untreated, into any waters of Florida Keys National Marine Sanctuary is prohibited. Sanctuary waters are a No-Discharge Zone.
  • Pumpout facilities for emptying holding tanks are available at marinas and mooring fields throughout Monroe County.

Fueling Your Boat

  • Be careful not to spill gas when fueling. Soak up spilled fuel with rags to prevent it from spilling into nearshore waters.
  • Discharging gasoline, motor oil, or oily bilge water into sanctuary waters is prohibited by sanctuary regulations.

Boat Maintenance and Repair

  • Keep your engine in good running condition and check for oil leaks on a regular basis.
  • Use environmentally friendly products for cleaning and washing. The U.S. Environmental Protection Agency certifies cleaning products that meet EPA Safer Choice standards.
  • Do not put harsh chemicals into boat drains where they are discharged as graywater.
  • Take steps to prevent hydraulic fluids, motor oil, and other chemicals from soaking into the ground or spilling into nearshore waters. Soak up spills with absorbent materials; dispose of rags with other hazardous wastes.
  • Dispose of batteries and waste oil at proper facilities in your community.
  • Support Florida's Clean Marina, Clean Boater, and Boatyard Programs.
An abandoned seat from a boat rests in shallow water.
Buoyant objects lost at sea often get caught in seaweed floating at the surface, or find their way to nearshore shallows. Photo: Scott Atwell/NOAA


  • Stow your trash in a secure container and dispose of it properly.
  • Use a boat hook or net to retrieve marine debris.
  • Food scraps don't belong in canals or sanctuary waters; they add nutrients that reduce water quality. Sanctuary regulations prohibit the depositing of materials such as food or trash into sanctuary waters.

Fishing and Cleaning Your Catch

  • Dispose of fishing line properly on land; recycle old line using designated bins. Fishing line, hooks, and plastics harm birds and sea turtles.
  • After cleaning your catch, dispose of fish scraps with your household waste in a secure container. Fish scraps add unwanted nutrients to nearshore waters that can help fuel harmful algal blooms.
  • Select fishing locations where you are less likely to entangle corals with your fishing line.