Polycyclic aromatic hydrocarbons(PAH) are a group of chemicals consisting of two or more six-sided rings of carbon which are fused together in various configurations. Shared electrons of the carbon atoms in the ring are the distinguishing feature of these compounds. Heteroatoms (nitrogen, sulfur or oxygen) in the ring structure and attached straight or branched chains of carbon and hydrogen can result in complex molecular structures. Each of these molecules have somewhat differing chemical reactivities and biological effects. Polycyclic molecular structures are formed when organic matter is exposed to high temperature for long periods of time and, once formed, are relatively difficult to degrade further (compared to common organic chemicals such as proteins, carbohydrates and lipids). These compounds tend to persist in the environment. PAH compounds reach the marine environment through a variety of routes including: pyrogenic sources from the incomplete combustion of fossil fuels (vehicles, home and industrial heating, electric power generation), forest and grass fires, creosote and asphalt, oil spills, natural seeps or erosion of ancient sediments, vehicle tire wear, and chronic small releases from a variety of petroleum product uses. Inputs to the coastal environment from these and other sources combine to create a very complex mix of hundreds of thousands of individual PAHs in the various environmental sectors such as sediments. Thus analyses of any ocean sample can focus only on a small subset of the PAH that might be found. Environmental concerns arise when loadings of PAH from combusting fossil fuels and careless handling of petroleum products exceed concentrations resulting from natural processes. Certain PAHs have been shown to cause human health problems and elevated concentrations in the habitat can have deleterious effects on marine species. Phenanthrene (3-rings) and pyrene (4-rings) are two typical petroleum components that when measured with other compounds can help to sort out issues such as sources, cycling and effects of oil in the coastal environment.

Polychlorinated biphenyls (PCBs) are among the environmental contaminants routinely analyzed. They include a possible 209 chemically related congeners of the biphenyl ring structure where a chlorine molecule has been substituted for hydrogen in one or more locations. Individual chlorobiphenyl congeners vary widely in their chemical reactivities and biological effects, depending on the numbers and locations of chlorine on ring. PCBs do not occur naturally and enter the environment via industrial synthesis and release from a variety of industrial uses. In the US, PCBs were sold as mixtures of congeners developed for their physical and electrical properties and were sold under the trade-name "Aroclor". Generally, PCBs are relatively resistant to degradation and their persistence and toxicity to humans and marine organisms led to restrictions in most countries. Through open-system applications and careless handling, many tons of PCBs have been lost to the environment. Physical-chemical properties of PCBs result in their sorption to and incorporation in sediments and they are found especially in urban harbors and downstream from industrial activities that produced or used them. For a variety of reasons, only selected congeners are cited in data reports. Concentrations of PCB #153 (a hexachlorobiphenyl) and PCB #101 (a pentachlorobiphenyl) are often reported because they are abundant components of commonly used commercial mixtures and pure congener standards are available for calibration.

Chlorinated Pesticides: The most famous (infamous) chlorinated pesticides are those of the DDT family of compounds (e.g., DDD- dichloro-diphenyl-dichloro-ethane,  DDE -  dichloro diphenyl dichloro ethylene, DDT - dichloro-diphenyl-trichloro-ethane.) Although their initial use offered pest and disease control benefits to society, the eventual realization that chlorinated pesticides demonstrate significant environmental persistence resulting in long-range global transport as well as toxicity to non-target organisms led to bans on their use in the US. Aldrin and heptachlor are two examples of "hard" pesticides that are no longer in use in the Gulf of Maine region. They are examples of the cyclodiene group of man-made chlorinated insecticides that were widely used in the 1950s - 60s to control a variety pests. Both chemicals have been shown to cause adverse biological reactions such as tumors in mammals. Although no longer used for pest control, these chemicals can still be detected in some marine sediments.