Issues Affecting the Bays

Decades ago, the Bays were thought to be generally healthy–clear waters with plentiful baygrass meadows, productive oyster reefs, and oxygen levels that supported diverse and plentiful fish populations. But years of accumulated nutrient pollution and habitat loss have changed the Bays to generally murky waters dominated by algae, have very few baygrasses or oysters, and do not support healthy oxygen levels in many areas. The changing climate is also of concern as rising seas, warming temperatures, and increased severity of coastal storms further threaten habitats and water quality.

Nutrient Pollution

Excess nutrient inputs remain the most significant issue facing the Inland Bays. Due to urbanization, agricultural activities, and low flushing rates, the Bays have become highly enriched with nitrogen and phosphorus. While these nutrients are essential for plant and animal growth, water quality can deteriorate when nutrients are present in excessive amounts. When that happens, algal growth accelerates and oxygen levels drop, making it difficult or impossible for organisms like fish or crabs to survive. The negative impacts associated with nutrient over-enrichment in the Bays mean there needs to be a reduction in nutrients entering waterways, as well as efforts to remove the nutrients already present.*

Habitat Loss

In addition to nutrient pollution, the loss of valuable aquatic, upland, and wetland habitats is also a stressor on water quality in the Inland Bays. Development on land, driven by rapid population growth, is increasing the acreage of impervious surface coverage. This land use change contributes to urban stressors such as encroachment by new developments on wetlands and tree canopy loss, which adds to urban pollution sources and stresses habitats. Underwater, wild oysters, and baygrasses are practically nonexistent, which means the Bays are without habitats that absorb excess nutrients, store greenhouse gasses like carbon dioxide, anchor sediments, protect shorelines from erosion, and provide refuge and nurseries for important species.

Climate Change

The Bays are also affected by climate change. Tidal wetlands are degrading due to sea-level rise and erosion. This is particularly concerning because the loss of wetlands reduces the capacity of the watershed to reduce flooding and erosion from storms, which are increasing in frequency and intensity. Rising temperatures mean that the growing season will continue to lengthen and the Bays will be warmer for a longer period each year. More rainfall and runoff could increase the transport of nutrients to the Bays, which can lead to conditions that create oxygen-depleting algal blooms.

Sea Level Rise

With the lowest mean elevation in the U.S. at just 60 feet, some coastal communities in Delaware are already experiencing the impacts of sea level rise.

Sea level rise is one of the primary effects of global climate change and one that is particularly significant for the state of Delaware. The state’s low average elevation and dependence upon coastal resources for jobs, tourism, and recreation make it particularly vulnerable to the impacts of sea level rise. These impacts include permanent flooding (or inundation) of wetlands and dry land, saltwater intrusion into freshwater supplies, and rising water tables. Rising sea levels will also increase the likelihood of flooding and damage during coastal storm events. The impacts of sea level rise will be felt statewide, as no part of the state is more than ten miles from tidal water.


Vibrio bacteria species occur naturally in estuaries and usually are harmless to humans. A small portion, however, can cause serious food-borne illness or wound infections. The species Vibrio vulnificus is the most lethal of these and the #1 cause of shellfish-associated fatalities in the U.S

Historically, in the U.S., V. vulnificus bacteria have mostly been found in the southeastern part of the country. But as sea surface temperatures rise, cases of V. vulnificus infections are becoming more common in places that used to be too cold for them to be common. Research completed at the University of Delaware shows that Vibrio bacteria may become more abundant in the Bays when some types of algae bloom in response to excess nutrients in the water.

As of February 2024, no cases of V. vulnificus have been reported in the Delaware Inland Bays.

There is no need to avoid the water, but take precautions to ensure your safe enjoyment of water recreation.

  • Wounds and water don’t mix–do not go into the water with a cut or open wound.
  • Wear water shoes to avoid getting cuts or scrapes on your feet.
  • Wear gloves when handling crab pots and other fishing equipment.
  • If you get a cut or abrasion, clean it immediately with soap and clean water. If soap and water aren’t readily available, clean it with hand sanitizer and then wash as soon as possible.
  • If your injury begins to show signs of infection (redness, swelling, or drainage), seek professional medical care immediately and let the provider know you recently had contact with natural waters. 
  • Always shower after swimming and wash your hands before eating.
  • Pay attention to beach closures and do not harvest shellfish from prohibited areas.
  • Cooking seafood kills associated bacteria. Do not consume raw oysters or clams if you are in a high-risk group (immunocompromised, liver disease, cancer, etc.)
  • Assess your own risk when it comes to swimming in natural waters. If you are immunocompromised in any way or prone to severe infections, it may be in your best interest to avoid swimming.

CDC information on vibriosis

*In December 1998, the Delaware Department of Natural Resources and Environmental Control set Total Maximum Daily Loads (TMDLs) for nitrogen and phosphorus for the Indian River and Rehoboth Bays. A TMDL was created for Little Assawoman Bay in December 2004.

TMDLs, as defined by the U.S. Environmental Protection Agency, calculate the maximum amount of a pollutant allowed to enter a waterbody so that the waterbody can meet water quality standards. A TMDL sets a “pollutant reduction target” and “load reductions” necessary to target the source(s) of the pollutant so that impaired waterways can once again be fishable or swimmable.

Water quality goals created in those TMDLs call for eliminating all “point sources” of pollution directly entering these water bodies. A “point source” could be something like an outfall pipe that sends treated stormwater or wastewater into the Bays and/or their tributaries. “Nonpoint sources” of pollution can include runoff from lawns or impervious surfaces, which does not come from an easily identified pipe or other source.

The TMDLs also require a 40% reduction in nonpoint phosphorus pollution in the Indian River, Rehoboth, and Little Assawoman Bays and a 65% reduction in the upper Indian River watershed; a 40% reduction of nonpoint nitrogen loading in the Indian River Bay, Rehoboth Bay, and Little Assawoman Bay and an 85% reduction in the upper Indian River watershed.