There is an on-going discussion on whether eutrophication is causing algal blooms and increased macrophyte growth, which are presumably causing documented secondary detrimental side effects (i.e., anoxia, loss of submerged aquatic vegetation, increase in jelly fish, decreases in fish and crab population, etc) in the Barnegat Bay, New Jersey. The discussion revolves around the fact that Barnegat Bay has historically been poorly drained, and that what we may see as current eutrophication effects

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... s only a part of natural conditions exacerbated by current nitrogen loading (i.e., with some of the negative affects coming from other stressors such as increased boat and jet ski traffic, bulkhead increases, loss of freshwater flows due to regionalization of upstream river sewerage treatment plants and loss through MUA ocean outfall, etc).The New Jersey Department of Environmental Protection (NJDEP) is evaluating the appropriate indices to be used to measure the ecosystem health of New Jersey's shallow, lagoonal estuaries or coastal bays. These would include bays such as Great Bay, Great Egg Harbor Bay, Absecon Bay, Ludlam Bay and Barnegat Bay. The federal government (USEPA and NOAA) has already developed a suite of indicators (e.g., EPA's National Coastal Assessment Report 2005 and NOAA's National Estuarine Eutrophication Assessment update) and has applied them to NJ's coastal bays with mixed results, especially as state level management tools, due to both geographic scale issues and the inability of the USEPA and NOAA metrics to identify proximate sources and causes of impairments.Further information is needed for NJDEP to develop water quality management tools; this study is designed to directly assist NJDEP in the development and/or enhancement of its nutrient criteria. There is growing consensus that the traditional macroinvertebrate indices used in EPA's EMAP and National Coastal Assessment may not be adequate to fully characterize the ecosystem health of shallow lagoonal estuaries such as those along the New Jersey [...]