NOAA's CHAMP is funded by the NOAA Coral Reef Conservation Program, which focuses mostly on three threats facing coral reefs today: climate change, effects of overfishing, and land-based sources of pollution. You can find more about the CRCP here. Below is brief introduction to land-based sources of pollution as it affects coral reefs, taken from that site.
Impacts from land-based sources of pollution (e.g. agriculture, deforestation, storm water, impervious surfaces,coastal development, road construction, and oil and chemical spills) on coral reef ecosystems include increased sedimentation, nutrients , toxins, and pathogen introduction. These pollutants and related synergistic effects can cause disease and mortality in sensitive species, disrupt critical ecological functions, cause trophic structure and dynamics changes (i.e. eutrophic conditions), and impede growth, reproduction, and larval settlement.
It is now well accepted that many major coral reef ecosystem stressors originate from land-based sources, most notably, toxicants, sediments, and nutrients. Within the United States and its jurisdictions, there are numerous locations where coral reef ecosystems are highly impacted by watershed alteration, run-off, and coastal development. The importance of identifying the extent of and reducing these effects has now become crucial, as land-based pollution and coastal development put 22 percent and 30 percent, respectively, of coral reefs on Earth at risk. The April 2004 Report of the US Commission on Ocean Policy highlighted the need for "an ecosystem and watershed-based management" approach to ocean pollution, and identified both "the astounding decline of coral reef ecosystems" and "an urgent need to address the identified, major factors causing coral declines."
The suite of problems facing coral reef ecosystems from land-based sources of pollution is broad and includes sediment, nutrients, and other pollutants from a variety of land-based activities that are transported in surface waters, runoff, groundwater seepage, and atmospheric deposition into coastal waters. There is compelling evidence that the sources have increased globally as a result of human-induced changes to watersheds. On the US islands in the Pacific and Caribbean, significant changes in the drainage basins due to agriculture, deforestation, feral grazing, fires, road building and other construction, and urbanization have in turn altered the character and volume of land-based pollution released to adjacent coral reef ecosystems. Many of these issues are further exacerbated due to specific characteristics exhibited in tropical island areas, all of which create unique management challenges when addressing issues related to land-based sources of pollution. A few examples include: high levels of rainfall; extreme weather events (hurricanes/ typhoons); highly erodible soils; limestone hydrologic features (Pacific atolls); and in some high islands, (American Samoa, Hawai`i), steep slopes abutting the coastal zone.
Sedimentation, including higher levels of suspended sediment in overlying waters, is commonly acknowledged to be one of the primary causes of coral reef ecosystem degradation. The combination of suspended, re-suspended, and deposited sediment act to limit coral growth, feeding patterns, photosynthesis, recruitment, and survivorship, as shown by numerous studies in a variety of settings. Other impacts of sediment include directly smothering and abrading coral. Although some corals can flourish in turbid water, such reefs are typically less diverse and are more restricted in depth ranges than those in clear water. To underscore this point, the US Commission on Ocean Policy reported that "pollution and run-off from coastal areas also deprive reefs of life-sustaining light and oxygen" and many Local Action Strategy (LAS) groups of the US Coral Reef Task Force have identified land-based pollution to reefs as a major area of concern.
In addition to sediment, land-based sources of pollution to coral reef ecosystems include pesticides, petroleum hydrocarbons, pharmaceuticals, heavy metals, pathogens, and excess nutrients. These pollutants can cause or exacerbate the deleterious effects of watershed transport of pollutant constituents onto coral reefs. Excess nutrients, including dissolved nitrogen and phosphorus from sewage, wastewater, and fertilizers, promote the growth of algae that compete with juvenile and adult corals for space on benthic reef surfaces and can affect success of coral settlement and in extreme cases can result in eutrophic conditions in reef waters. In addition, land-based inputs may both directly contribute land-derived pathogens and/or exacerbate the effect of in situ pathogens on coral reef ecosystems.
Finally, the local impacts of land-based sources of pollution work in synergy with global and regional threats such as climate change, land use practices, and freshwater inputs, magnifying the effect of both types of stressors. In particular, the potential for increased frequency and intensity of storm events associated with climate change could exacerbate run-off of sediment and other pollutants.