In the USA, road salt usage in urban areas has increased since the 1950s. In the greater Chicago area over 175 000 tons of salt are applied every year. The salt runoff from this application has the potential to negatively impact nearby plants and alter native plant communities. We evaluated how varying salt concentrations affect overall germination, germination probability, and multiple metrics of germination speed for seeds from five source populations of Thuja occidentalis L. Two populations in a native forested fen system are susceptible to salt runoff from the Illinois Tollway. We found that increased salt concentrations decreased both the probability of germination and overall germination, and increased the time to germination. Seeds from the two natural populations performed poorly compared to the other populations. Salt pollution impacts the health and survival of adult trees, and may also inhibit the reproduction and recruitment of T. occidentalis. Reduction of salt pollution is necessary to maintain the long-term survival and persistence of this species, other sensitive species, and native fen habitats.