Our Human Footprint

How do nutrients & microbes affect water quality?

Changes in land use during the past 60 years or more have affected water quality by increasing the delivery of land-derived nutrients such as nitrogen (N) and phosphorus (P) and microbes (bacteria and viruses) to coastal estuaries.  These changes in water quality can affect the ecosystem, human health, and local economies that depend on clean water. 


Nutrients such as N and P are essential for life, but in excess they can cause an imbalance in water quality, including:

  • Excessive growth of primary producers (such as phytoplankton and macroalgae) and buildup of organic matter in the water and sediments, which is known as eutrophication.
  • Initially, excess phytoplankton and macroalgae may provide more food for some animals, including shellfish.
  • Excess phytoplankton and macroalgae in the water column can shade seagrasses that need light for growth.
  • The increased organic matter in the water and sediments stimulates use of oxygen by animals and microbes. 
  • High organic matter and low oxygen can lead to stressful conditions and death of some aquatic animals, including fisheries species, creating “dead zones” in coastal areas.


Microbes, such as bacteria and viruses, are a natural part of the marine community, but some microbes carried by human wastewater and stormwater can make people sick.

  • To protect people from illness due to consumption of pathogens in raw shellfish, state and federal officials monitor the water for fecal-indicator microbes associated with illness, such as fecal coliforms and E. coli
  • Water bodies with high concentrations of indicator microbes are seasonally or permanently closed to shellfishing. 
  • Most seafood-related illnesses are caused by bacteria such as Vibrio, Salmonella, Shigella, and Listeria, which may or may not be conveyed by wastewater. The wastewater-associated virus that is most commonly related to seafood-borne illness is Norovirus.  
  • Illness can best be prevented by consuming properly stored, cleaned, and prepared seafood from approved areas and sold by reliable vendors (for more information on seafood safety, click here).

Where do nutrients & microbes come from?

Stormwater, sewage, septic systems, road runoff, and industrial wastewater are known sources of anthropogenic nutrients and microbes to coastal waters.

Outfall Pipes

An outfall pipe is a location where stormwater or wastewater discharges into a body of water.  Outfall pipes are commonly seen along the edge of most rivers, estuaries and even in marshes. Outfall pipes deliver fertilizers, animal waste, road runoff, chemical contaminants and other debris via stormwater, and some homes have unpermitted connections to stormwater drains.  Wastewater treatment facilities and many industries are permitted to discharge wastewater into rivers, streams, estuaries and coastal waters. These permits require stringent testing and documentation that pollutant concentrations are within regulations. Permits are regulated under the Clean Water Act and can be viewed online.

Did you know: Most stormwater drains empty into local streams and rivers that discharge to bays and estuaries without treatment. Sewage is typically treated before discharge to reduce potentially harmful microbes but may not be treated to remove nutrients.  Sewage treatment can occur at the level of the individual home, neighborhood, or municipality, with some communities served by a combination of treatments.  Industrial wastewater is often treated to normalize salinity and pH, but may not remove nutrients. Combined sewer overflows can occur when systems collect rainwater runoff, sewage, and industrial wastewater in the same system of pipes for transportation to a wastewater treatment plant for treatment and discharge. During periods of high rainfall or snowmelt, the volume of wastewater can exceed the capacity of the treatment facility, resulting in overflow and discharge of some untreated wastewater. 

For more information on combined sewage overflows visit: https://www.epa.gov/npdes/combined-sewer-overflow-frequent-questions

Failing Infrastructure

Failing septic systems and pumping stations can leak untreated wastewater into groundwater, streams and estuaries. Just like any other structure or equipment, septic systems and wastewater treatment facilities require regular maintenance and periodic upgrades or replacement to ensure proper operation and function.   Severe storms can also damage these structures, which is a particular problem on the Gulf of Mexico coast.  

Did you know: According to the American Society of Civil Engineers (ASCE), which evaluates wastewater infrastructure in the U.S., “…wastewater treatment plants are the most basic and critical infrastructure systems for protecting public health and the environment.”  Currently wastewater infrastructure in the U.S. is rated as D+; nationwide improvements are needed.  About 850 billion gallons of untreated sewage and stormwater are released to US waters each year, and demand on wastewater treatment plants is expected to increase 23% by 2030. 

For more information and to read the ASCE Wastewater Report Card visit:


Overboard Discharge

Houseboats, commercial and recreational vessels, and fish camps can be sources of sewage that deliver microbes such as E. coli and fecal coliforms to the water.  The Clean Water Act regulates sewage release from vessels. It is illegal to discharge untreated waste to rivers or streams and within 3 miles of shore. Boaters must have an onboard treatment device or holding tank and pump out wastewater at an approved location on shore. States also may designate ‘No Discharge Zones’ that further restrict where and how boat sewage may be released.

Did you know: A recent survey in a recreational area in Bermuda found that as many as 60% of boat owners typically dump untreated waste overboard and nearly 40% were unaware that overboard sewage dumping is an environmental concern.  According to another study by the California State Water Resources Control Board, discharge from one boat during one weekend contributes the same amount of bacteria to the water as treated sewage from 10,000 people.

For more information on vessel-related sewage and options for disposal visit: 

Non-point Sources

Runoff, seepage, and drainage can convey nutrients and microbes to rivers and estuaries from a combination of different sources on land, which are collectively referred to as non-point sources.  Impervious surfaces such as roads, parking lots, driveways, sidewalks, and buildings change local hydrology and increase the volume and intensity of downstream flows.  These flows flush nutrients, microbes, oils, chemicals, sediments, and debris from roads and nearby areas directly to local streams and ultimately into estuaries and the ocean.  Some other non-point sources common to the northern Gulf of Mexico include agricultural run-off from livestock or crop lands and wildlife and pet waste.

Did you know: Most of the world’s largest cities are on the coast, and urban runoff has been recognized as the leading cause of human-related water pollution for nearly two decades. Impervious surface area, therefore, is a useful indicator of water quality and is often more easily measured than other sources of nutrients and microbes.

Click for more information on:
1) Impervious surfaces and how you can reduce urban runoff 
Urban Areas
Protecting Water Quality from Urban Runoff: Factsheet

2) Managing pet & wildlife waste
Learn how one community encourages citizens to “Scoop the Poop!” to improve water quality.
Prevent contamination of drinking water

3) Managing livestock waste


Photo caption: Some sources of nutrients (such as nitrogen) to local estuaries include septic systems, atmospheric deposition, fertilizer, and direct discharge from stormwater drains and wastewater treatment plants (image modified from Valiela et al. 2000 Biogeochemistry 49:277-293).

Read about local water quality issues:
Mobile Bay Magazine: Saving the Bay
Grand Bay NERR Water Quality workbook
Mobile Bay National Estuary Program's State of the Bay 2008
Create a Clean Water Future Campaign







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