The heavily urbanized and industrialized Baltimore Harbor/Patapsco River/Back River system is one of the most highly contaminated regions of the Chesapeake Bay. In June 1996, surficial sediments were collected at 80 sites throughout the subestuarine system, including historically undersampled creeks and embayments. The samples were analyzed for a suite of hydrophobic organic contaminants (HOCs) consisting of 32 polycyclic aromatic hydrocarbons (PAHs) and 113 polychlorinated biphenyl (PCB) congeners. Total PAH and total PCB concentrations ranged from 90 to 46,200 and 8 to 2,150 ng/g dry weight, respectively. There was enormous spatial variability in the concentrations of HOCs, which was not well correlated to grain size or organic carbon content, suggesting nonequilibrium partitioning and/or proximity to sources as important factors explaining the observed spatial variability. High concentrations of both classes of HOCs were localized around major urban stormwater runoff discharges. Elevated PAH concentrations were also centered around the Sparrow's Point Industrial Complex, most likely a result of the pyrolysis of coal during the production of steel. All but 1 of the 80 sites exceeded the effects range‐low (ERL) for total PCBs and, of those sites, 40% exceeded the effects range‐medium (ERM), suggesting toxicity to marine benthic organisms would frequently occur. Polychlorinated biphenyl homolog patterns most closely resembled Aroclor 1260 at sites around areas of high concentration of industrial outflows and urban runoff. Conversely, those sites further from suspected municipal and industrial discharges had patterns resembling that of Aroclor 1254. We suggest the heavier chlorinated pattern is indicative of near‐source emissions of PCBs. The lighter chlorinated PCB patterns observed are similar to those found in mainstem Chesapeake Bay sediments and may reflect a more weathered pattern or one derived, in part, from air‐water exchange of gaseous PCBs. Using principal component analysis, differences in PAH signatures were discerned. Higher molecular weight PAHs were enriched in signatures from sediments close to suspected sources (i.e., urban stormwater runoff and steel production complexes) compared to those patterns observed at sites further from outfalls or runoff. Due to varying solubilities and affinities for organic matter of the individual PAHs, partitioning of the heavier weight PAHs may enrich settling particles with high molecular weight PAHs. Lower molecular weight PAHs, having lower affinity for particles, may travel from the source to a greater extent.