Extensive industrial areas in headwater stream watersheds can severely impact the physical condition of streams and introduce contaminants. We compared 3 streams that received stormwater runoff and industrial effluents from industrial complexes to 2 reference streams. Reference streams provide a benchmark of comparison of geomorphic form and stability in coastal plain, sandy‐bottomed streams as well as concentrations of trace elements in sediment and biota in the absence of industrial disturbance. We used crayfish (Cambarus latimanus, Procambarus raneyi, Procambarus acutus) and crane fly larvae (Tipula) as biomonitors of 15 trace elements entering aquatic food webs. Streams with industrial areas were more scoured, deeply incised, and less stable. Sediment organic matter content broadly correlated to trace element accumulation, but fine sediments and organic matter were scoured from the bottoms of disturbed streams. Trace element concentrations were higher in depositional zones than runs within all streams. Despite contaminant sources in the headwaters, trace element concentrations were generally not elevated in sediments of the eroded streams. However, element concentrations were frequently elevated in biota from these streams with taxonomic differences in accumulation amplified. In eroded, sand‐bottomed coastal plain streams with unstable sediments, single snapshots of sediment trace element concentrations did not characterize well bioavailable trace elements. Biota that integrated exposures over time and space within their home ranges better detected bioavailable contaminants than sediment. Environ Toxicol Chem 2019;38:115–131. © 2018 SETAC