The Great Lakes have been the focus of extensive environmental research, but recent data on the aquatic concentrations of emerging compounds, such as flame retardants, are scarce. Water samples from 18 stations on the five Great Lakes were collected in 2011 and 2012 using XAD-2 resin adsorption and analyzed for PCBs, organochlorine pesticides, PAHs, polybrominated diphenyl ethers (PBDEs), and emerging flame retardants, including organophosphate flame retardants (OPEs). Total PCB concentrations ranged from 117 ± 18 pg/L in Lake Superior to 623 ± 113 pg/L in Lake Ontario. Among the organochlorine pesticides, the most abundant was dieldrin, with the highest average concentration of 99 ± 26 pg/L in Lake Erie, followed by p,p′-DDD with an average concentration of 37 ± 8 pg/L in Lake Ontario. Total PAH concentrations were higher in Lakes Erie and Ontario than in Lakes Michigan, Huron, and Superior. Total PBDE concentrations were highest in Lake Ontario (227 ± 75 pg/L), and the most abundant congeners were BDE-47, BDE-99, and BDE-209. Total OPE concentrations ranged between 7.3 ± 4.5 ng/L in Lake Huron to 96 ± 43 ng/L in Lake Erie.