More than 2 million tons of chromium ore processing residue (COPR) waste was disposed of in Hudson County of New Jersey, which was known as the center of the production of chromate in the 20th century. The Cr(VI) removal experiments were conducted with the hyporheic zone (HZ) sediments collected along the shore of an urbanized estuary located in and near Hudson County to investigate the natural remediation of Cr(VI). Fine-grained and organic-rich Passaic River sediments showed the highest removal capacity for Cr(VI), whereas the lowest removal of Cr(VI) occurred in coarse-grained and organic-poor sediments from Newark Bay. In general, Cr(VI) removal increased with higher amounts of sediment organic matter, sulfur, and silt and clay fractions, as well as lower pH conditions. The removal of hexavalent chromium in organic-rich sediments is attributed mainly to the reduction of Cr(VI) to Cr(III), resulting in less reversible immobilization of Cr(VI), while reversible adsorption could also remove Cr(VI). The results suggest that the organic-rich, fine-grained HZ sediments can act as a natural reactive barrier for the remediation of Cr(VI) transport from subsurface to surface water in the estuary. Further research is needed to understand the long-term mobility of Cr along the urban estuary.