The Lower Fox River is a 39 mile section which supports approximately 270,000 rural inhabitants across 18 counties, 303,000 metropolitan residents in Green Bay and Appleton, Wisconsin, and several large industrial complexes such as paper mills and power plants. This paper presents the distribution and concentrations of aliphatic (n-alkanes) and aromatic hydrocarbons (polycyclic aromatic hydrocarbons [PAHs]) as well as total organic carbon (TOC) in the Lower Fox River to identify the sources of hydrocarbon contamination. Excluding one outlier, percent TOC values were between 0.73 and 19.9% with an average value of 6.74%. Total n-alkanes ranged from 3.51 μg/g to 117 μg/g and showed a strong presence of odd carbon-numbered n-alkane ratios (range of C25 to C35), suggesting source input from terrestrial biomass. The mean polycyclic aromatic hydrocarbon (PAH) concentration was 24,800 ng/g. High molecular weight PAH concentrations dominated the distribution of hydrocarbon contaminants. Cross-plots of PAHs were used to compare diagnostic source ratios of benz[a]anthracene (BaA), chrysene (Chr), fluoranthene (Flu), pyrene (Pyr), anthracene (Ant), phenanthrene (Phe), indeno[1,2,3-cd]pyrene (InP), and benzo[g,h,i]perylene (BghiP) by depth and area. PAH ratios varied slightly with the core depth. Deeper core sections indicated the presence of biomass combustion while the upper core sections indicated combustion of both petroleum and biomass. The PAH toxicity of one core was estimated using toxicity equivalency factors, and the benzo[a]pyrene toxic equivalence quotient totaled 2,293 ng/g-dry wt. Levels of PAHs in sediments are compared with established regulatory values and recommendations are made.