Railway transport of coal poses an environmental risk because coal dust contains polycyclic aromatic hydrocarbons (PAHs), mercury (Hg), and other trace metals. In the Pacific Northwest, proposed infrastructure projects could result in an increase in coal transport by train through the Columbia River corridor. Baseline information is needed on current distributions, levels, and spatial patterns of coal dust-derived contaminants in habitats and organisms adjacent to existing coal transport lines. To that end, we collected aquatic surface sediments, aquatic insects, and juvenile fish in 2014 and 2015 from Horsethief Lake State Park and Steigerwald National Wildlife Refuge (NWR), both located close to the rail line and within the Columbia River Gorge National Scenic Area. Two subsites in each area were selected: one close to the rail line and one far from the rail line. Detected PAH concentrations were relatively low compared to those measured at more urbanized areas. Some contaminants were measured at higher concentrations at the subsites close to the rail line, but it was not possible to link the contaminants to a definitive source. Trace metal concentrations were only slightly higher than background concentrations, but a few of the more sensitive benchmarks were exceeded, including those for As, Pb, and Se in fish tissue and fluoranthene, Cd, Cu, Mn, Ni, Zn, Fe, and As in sediments. At Horsethief Lake, Chinook salmon and yellow perch showed lower total mercury body burdens than other species, but PAH body burdens did not differ significantly among species. Differences in the species caught among subsites and the low number of invertebrate samples rendered food web comparisons difficult, but these data show that the PAHs and trace metals, including mercury, are accumulating in these wetland sites and in some resident organisms.