Sources of polycyclic aromatic hydrocarbons (PAHs) in the Black River and Ashtabula River sediments were apportioned using a factor analysis (FA) model with nonnegative constraints. Source profiles, contributions (microg/g) and percent contributions are determined with no prior knowledge of sources. The FA model includes scaling and backscaling of data with average PAH concentrations, without sample normalization. The present work is a follow-up to studies that used a chemical mass balance model to apportion sources to the same data sets. Literature source profiles, modified based on gas/particle partitioning of individual PAHs, from nine PAH sources were considered for comparison. FA results for a three-source solution indicate traffic (58%), coke oven (26%), and wood burning/coal tar (16%) are the primary PAH sources to Black River sediments. The primary PAH sources to the Ashtabula River sediments are traffic (51%), coke oven (44%), and wood burning (5%). This work supports the previous studies of Black River and Ashtabula River PAHs by CMB model. In addition, FA provides a more realistic fit to Ashtabula River model data by eliminating 100% contributions from one source.