In this paper, we present our study of the speciation of copper and hexavalent chromium sorbed onto a lignocellulosic substrate, using analytical microscopy. The lignocellulosic substrate constitutes a low-cost biomaterial that can be used in wastewater treatment. Transmission electron microscopy (TEM) coupled with energy-dispersive X-ray spectroscopy (EDXS) was used to determine the speciation of the two metal ions on the constitutive moieties of the lignocellulosic substrate. The use of a staining agent sensitive to carbon unsaturation allowed us to differentiate between the microstructures rich in lignin entities and those rich in cellulose entities. The EDX analysis showed that metal ions are preferentially sorbed onto microstructures rich in lignin moieties. The energy electron loss spectroscopy (EELS) was used to determine the oxidation states of chromium in association with lignocellulosic moieties. We showed that the sorption process of hexavalent chromium requires the reduction of Cr(VI) into Cr(III) and the probable oxidation of lignin moieties.