Industrial, agricultural and other anthropogenic activities have lead to the introduction of thousands of pollutants, most of them synthetic organic compounds to the marine environment (Dachs and Méjanelle 2010). A fraction of these organic compounds, called persistent organic pollutants (POPs), are chemicals that have become a major concern because of their toxicity, persistence, bioaccumulation tendency, and susceptibility to undergo long-range atmospheric transport. Traditionally, much attention have been given to a few families of POPs, such as polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs) such as DDT and hexachlorobenzene (HCB) and other byproducts of industrial processes or combustion such as dioxins and furans (PCDD/Fs) and polynuclear aromatic hydrocarbons (PAHs). However, these chemicals are a small fraction of the total known pollutants in the marine environment (Dachs and Méjanelle 2010) and presumably of the total potential pollutants occurring in the environment (Muir and Howard 2006). In any case, these few families of POPs have been detected everywhere on earth in abiotic and biotic matrices (Gioia et al. 2006, 2008a; Gilman et al. 1997; Jaward et al. 2004). Today, compounds with similar or different physical chemical properties (such as the polybrominated diphenyl ethers, PBDE and other fluorinated compounds, PFs) are being manufactured and widely used, potentially entering the environment and providing new challenges for the maintenance of its quality. Our current knowledge indicates that the cycling of these chemicals in the environment is highly complex; indeed their local, regional and global cycle is controlled by repeated air-surface exchange and interactions with the carbon cycle, especially the organic and soot carbon fractions. Because, a fraction of these chemicals are hydrophobic, they have the potential to accumulate in all the trophic levels of ecosystems, including those far away from sources. The number of known organic pollutants in marine waters, and other environmental compartments, has increased dramatically during the last decade, in part due to important analytical developments. Nowadays, even though much of our knowledge on organic pollutants is centered on a few chemical families (PCBs, HCHs, DDT, PAHs, etc.), these families should be viewed as markers or “surrogates” of other pollutants in marine waters with similar physical–chemical properties. In addition, other chemicals with different physical–chemical properties (i.e., greater water solubility, low volatility) may reach coastal and open oceans via rivers and undergo different environmental behavior, due to their ionic character. In fact, some of newly emerging compounds have been suggested to behave as passive tracers in waters (Yamashita et al. 2008), a behavior quite different from that shown by legacy POPs such as PCBs or HCHs.