The sediment distribution of per- and polyfluoroalkyl substances (PFAS) along a river to ocean transect was investigated. Samples were collected between September 2017 and October 2019 with targeted quantification of six legacy and replacement PFAS by LC-MS/MS. Total PFAS concentrations ranged from below the LOQ to 7.47 ng per g dry weight with PFOA, PFOS, HFPO-DA and PFMOAA the most frequently detected. Significant correlations (p < 0.05) were found between PFOS and HFPO-DA sedimentary concentration and percent organic carbon (% OC); however, PFOA and PFMOAA were not correlated with sediment % OC. This study highlights the occurrence of the replacement PFAS in sediments for the first time. Sediment extracts were screened for 18 additional PFAS compounds by high resolution mass spectrometry. A series of perfluorinated ether carboxylic acid and perfluorinated ether sulfonic acid with either one or two acidic functional groups were detected at various locations in the upper portion of the Cape Fear River. A series of chromatographically resolved isomers (C7F13O5S1; M-1) were detected and may be Nafion™ degradation products.