Thousands of chemicals are introduced to market every year with little or no regulatory oversight or understanding of their impact on human health or the environment. These compounds, known as chemicals of emerging concern (CECs), have widespread in bay sediment, however, their identification has traditionally been challenging due to the complexity of this environmental matrix. This study was designed to identify and prioritize CECs in the San Francisco Bay. We hypothesized that CECs would be significantly more abundant in margin sediment than ambient sediment. In this study, a total of 8 margin sediment samples (5 Lower South Bay and 3 Extreme Lower South Bay) and 3 ambient sediment samples were prepared using a modified QuEChERS method. The final extracts were analyzed by non-targeted analysis based on comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC/TOF-MS). A total of 401 compounds were detected at 50% or more of at least each group of marginal sediment samples (5 Lower South Bay sites and 3 Extreme Lower South Bay sites). 172 compounds were tentatively identified. Of these, 33 compounds were found only in margin sites and 52 compounds were found to be significantly more abundant in the margin sites. These 85 compounds fell into 31 distinct compound classes. These compounds were prioritized by their persistence, bioconcentration, and toxicity (PBT) characteristics and occurrence data, yielding 22 priority compounds in 6 compound classes. A variety of (o-, s-, n-) substituted PAHs, alkylated PAHs, and PAH derivatives were found in this study. The legacy contaminant p,p’-DDE was found, indicating an existing reservoir or new source of this compound feeding the Bay. The sample site with the most compounds detected (81/85) was the only site near an airport, heavy industry, a golf course, and waste water treatment while the site with the fewest compounds detected (35/85) was one of only two sites with fewer anthropogenic contributions, demonstrating a correlation between proximity to these entities and total compounds detected. Only 2 of the 85 high ID compounds identified are routinely monitored in the Bay; highlighting a major monitoring gap and need for regulatory update. Three appendices are attached.