Muscle tissue and organ samples of six different fish species were collected from ten locations in Southeast Michigan's Huron and Rouge watersheds. Per- and polyfluoroalkyl substances (PFAS) were analyzed in 36 samples comprising filets, liver, gut, and eggs using targeted analysis and the direct total oxidizable precursor (dTOP) assay on a subset of six samples. The median concentrations of the ∑PFAS in filets from the Huron and Rouge watersheds were 13 and 6.3 ng/g wet weight (w.w.), respectively. Perfluorooctane sulfonate (PFOS) was the most detected and abundant compound in fish organs, with the liver having the largest overall burden of PFAS. The highest percent increase in targeted PFAS after the dTOP assay was observed in the Catfish filet (552%) while the smallest increase was in the Catfish liver (32%) accounting for 1.3 and 8.1 nMole F/g dry weight (d.w.), respectively. The positive matrix factorization (PMF) analysis revealed three distinct PFAS sources, of which the one attributed to PFOS explained 73% of the data. Results from this work have important implications for fish consumption in Michigan waterways. Among the filet samples analyzed, the calculated daily consumption limit of total PFOS was exceeded in approximately 82% and 91% of samples for adults and children over the age of seven years old, respectively.