A new electrochemical sensor based on molecular imprinting technology was developed, for rapid and sensitive detection of the odorous substance geosmin (GSM) in water. In this method, the molecularly imprinted membrane was successfully modified on the surface of the glassy carbon electrode (GCE) using the electrochemical deposition method. In the presence of the target analyte (geosmin), the target analyte occupies the detection site and the detection signal will attenuate. As the concentration of the target analyte increases, the attenuation of the electrical signal becomes more pronounced. This sensor can quantitatively detect geosmin at concentrations as low as 5 ng/L, which is currently the lowest limit of detection (LOD) for GSM detection by an electrochemical sensor in reported studies. The modified GCE provided an analytical curve for GSM detection in the range of 5–200 ng/L.