This dataset provides baseline concentrations (from 2014) of polycyclic aromatic hydrocarbon (PAH), other aromatic organic compounds, mercury (Hg), and trace metal concentrations in sediment and biota collected from two sites along an existing rail line used for coal transport in the Columbia River Gorge, Washington. For this study, aquatic surface sediments, aquatic insects, and juvenile fish were collected in 2014 from Horsethief Lake in Columbia Hills State Park and Steigerwald Lake National Wildlife Refuge (NWR), both located in close proximity to the rail line and within the Columbia River Gorge National Scenic Area. Samples were collected from two subsites in each area: one closer to the rail line and one farther from the rail line. Fish species collected for analysis included anadromous salmonids and resident yellow perch, sculpin, pumpkinseed, northern pikeminnow, and smallmouth bass.