Abstract Per- and polyfluoroalkyl substances (PFAS) are thousands of toxic synthetic chemicals that bioaccumulate and persist in the environment. They are known to cause immunotoxicity, organ damage, endocrine disruption, and reproductive impairments in wildlife such as sea otters (Enhydra lutris). However, there is limited information on the distribution of these chemicals across the northeastern Pacific, and baseline data are missing to assess their potential impacts on sea otters in regions such as British Columbia (BC), Canada. We analyzed liver (n = 11) and skeletal muscle samples (n = 5) from 11 deceased sea otters from coastal BC using the U.S. Environmental Protection Agency method 1633 with ultrahigh performance liquid chromatography coupled to a triple quadrupole mass spectrometer. We found 8 of the 40 tested PFAS were present in all sampled sea otters, although concentrations of each PFAS varied between individuals. Sea otter livers contained more PFAS compounds at higher total average concentrations than skeletal muscle (i.e., 8 PFAS totaling 10.38 ng/g wet wt vs. 1 PFAS totaling 0.38 ng/g wet wt). Only perfluorooctanesulfonamide (PFOSA) was identified in both liver and muscle tissues, whereas the remaining 7 PFAS were unique to the liver. The three PFAS that dominated the liver PFAS composition (perfluorononanoic acid, PFOSA, and perfluorooctanesulfonic acid) accounted for 84% of the contaminant load in the livers. Geographically, PFAS concentrations were more than three times higher on average in sea otters recovered near major cities and shipping routes. Identifying the contaminants accumulating in sea otters provides insights into the health threats confronted by recovering sea otter populations. Our study also establishes baseline PFAS contamination levels in BC sea otters, which can be used to monitor and regulate the presence of PFAS on marine environments in western Canada.