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The development of ultra-sensitive methods for detecting anions is limited by their low charge to radius ratios, microenvironment sensitivity, and pH sensitivity. In this paper, a magnetic sensor is devised that exploits the controllable and selective coordination that occurs between a magnetic graphene quantum dot (GQD) and fluoride anion (F-). The sensor is used to measure the change in relaxation time of aque-ous solutions of magnetic GQDs in the presence of F- using ultra-low-field (118 μT) nuclear magnetic resonance relaxometry. The method was optimized to produce a limit of detection of 10 nmol/L and then applied to quantitatively detect F- in domestic water samples. More importantly, the key factors respon-sible for the change in relaxation time of the magnetic GQDs in the presence of F- are revealed to be the selective coordination that occurs between the GQDs and F- as well as the localized polarization of the water protons. This striking finding is not only significant for the development of other magnetic probes for sensing anions but also has important ramifications for the design of contrast agents with enhanced relaxivity for use in magnetic resonance imaging.