NOAA’s National Status and Trends (NS&T) Mussel Watch Program conducted regional pilot studies to assess the magnitude and distribution of contaminants of emerging concern (CEC) in shellfish and sediment from different coastal zones. In 2015, oyster and surficial sediment samples from study areas in the Chesapeake Bay, Maryland, and Charleston Harbor, South Carolina were assessed for CECs, such as pharmaceutical and personal care products (PPCPs), current use pesticides, flame retardants, new industrial chemicals, stain resistant compounds, and endocrine-disrupting chemicals. Results indicated that CECs are being accumulated at various degrees in coastal resources and the environment. Classes of CECs most frequently detected in oyster tissues and sediments from both study areas were the perfluorinated compounds (PFCs), the flame retardants (polybrominated diphenyl ethers; PBDEs), and current use pesticides. In the Chesapeake Bay, at least one PFC and PBDE flame retardant was detected in all sediment samples. In Chesapeake Bay sediment samples, PFCs and PBDEs were detected in 40% and 21%, respectively, of all measurements (considering both numbers of compounds and numbers of samples). In contrast, alternative (non-brominated) flame retardants had the lowest frequency of detection of all CEC classes. The highest concentrations of CECs detected in Maryland oyster tissues were found to be associated with the pharmaceuticals prednisone (144,000 pg/g wet mass), hydrocortisone (47400 pg/g wet mass), and acetaminophen (23,300 pg/g wet mass). However, PPCPs were detected far less frequently than PBDEs and PFCs in Maryland tissue and sediment. At least one CEC was detected at each South Carolina station for both sediment and oysters samples. In Charleston Harbor samples, CEC detection frequencies followed a similar overall pattern as in Chesapeake Bay. Perfluorinated compounds (PFCs) were the most frequently detected CECs, at 16.7% and 11.1% in sediments and oysters respectively. The flame retardants (PBDEs) were also often detected in both sediments and oysters in South Carolina samples. The highest concentrations reported in Charleston Harbor sediments, however, were for current use pesticides, specifically the pyrethroid insecticides permethrin (6,890 ng/g dry mass) and cypermethrin (1,590 ng/g dry mass). Overall occurrence and distribution of some CEC chemicals appeared to be associated with land use categories in the watershed adjacent to the survey sites. Although further study is required to confirm this association, in general, the number of reported concentrations at urban sites was elevated compared to the suburban sites in both study areas. The same relative numbers were observed between suburban and undeveloped (or Reference) sites.