Of the NCA components, one of the more interesting for New Jersey's estuarine waters is the sediment quality assessment. Sediment quality is an important measure of the health of an estuary. A wide variety of metals and organic substances, such as polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and pesticides, are discharged into estuaries from urban, agricultural, and industrial sources in the watershed.

The contaminants adsorb onto suspended particles and eventually accumulate in depositional basins. If contaminants accuummulate to significant levels they can disrupt the benthic community of invertebrates, shellfish, and crustaceans that live in or on the sediments. To the extent that the contaminants become concentrated in the organisms, they pose a risk to organisms throughout the food web—including humans.