There are few effective technologies for the sequestration of highly water-soluble pertechnetate (TcO4−) from contaminated water despite the urgency of environmental and public health concerns. In this work, anion exchanged and cetyltrimethylammonium bromide (CTAB) functionalized MIL-101-Cr-NO3 were investigated for perrhenate (ReO4−), a surrogate of TcO4−, sequestration from artificial groundwater. Cl−, I−, and CF3SO3− exchanged MIL-101-Cr proved more effective at ReO4− removal than the parent MIL-101-Cr-F. Compared to the parent framework, CTAB functionalized MIL-101-Cr-NO3 increased ReO4− removal capacity from 39 to 139 mg/g, improved the reaction kinetics from ~30 to <10 min to reach full adsorption capacity and the selectivity for ReO4− over competing NO3−, CO32−, SO42−, and Cl−. Spectroscopic data indicated that the chemical speciation of Re in the exchanged MIL-101-Cr remained ReO4−, indicating synergistic sequestration through both anion exchange and non-ion exchange binding with the positively charged ligand of CTAB. These studies foreshadow potential applications of MOFs for the remediation of 99TcO4− from contaminated environments.