Generally, the nations most contaminated estuaries are in highly urban areas such as those around the Mid-Atlantic coast. Chemical contaminants of coastal waters include inputs from municipal and industrial waste water, agricultural waste water, agricultural pesticides and fertilizers, animal waste, urban nonpoint sources, storm water runoff, and atmospheric deposition. Estuarine and coastal lands and waters are used for many purposes that often result in conflicts for space and resources. Some uses may result in the absolute loss or long term degradation of the general aquatic environment or specific aquatic habitats, and pose theoretically significant , but as yet unquantified, threats to scup and their habitats. This increase in habitat degradation plays and important role in scup population health.
Coastal areas are vitally important as feeding, spawning, and nursery grounds for scup.
However, population shifts to coastal areas and associated industrial and municipal expansion have accelerated competition for use of the same habitats. As a result, these habitats have been substantially reduced and continue to suffer the adverse effects of dredging, filling, coastal construction, energy development, pollution, waste disposal, and other human related activities. It is obvious that new systems are needed to conserve habitats and living marine resources, while facilitating the completion of necessary, compatible economic developments. Each state should implement protection for scup habitat within its jurisdiction in order to ensure the sustainability of that portion of the spawning stock that either is produced or resides within its boundaries. Such a program should inventory historical habitats, identify habitats presently used and specify those that are targeted for recovery, and impose or encourage measures to retain or increase the quantity and quality of scup essential habitats.