Multilayered reduced graphene oxide (rGO) was functionalized with amino groups by treatment with nitrogen plasma. Raman spectroscopy showed plasma treatment not to substantially alter the chemical structure of rGO and that a wide range of functional nitrogen groups is evenly incorporated into the carbon lattice. The amino-modified rGO was used to design an electrochemical biosensor in which a DNAzyme, substrate DNA and Pb(II) and Hg(II) binding DNA were immobilized on the amino-rGO placed on a gold electrode. The high concentration of amino groups and the rough surface of the rGO favor DNA immobilization. Heavy metal ions are bound to the surface via specific interaction between DNA and the two ions which are detected by electrochemical impedance spectroscopy at a potential of 0.2 V (vs. Ag/AgCl). The detection limits for Pb(II) and Hg(II) are as low as 7.8 and 5.4 pM, respectively, and the analytical ranges extend from 0.01 to 100 nM. The sensor is highly specific and stable and therefore represents a highly promising tool for use in environmental monitoring.