The Heterodyne Instrument for the Far-Infrared (HIFI) is one of three instruments to be launched aboard the Herschel Space Observatory (HSO) in 2009. HIFI will provide unprecedented spectral sensitivity and resolution between 490–1250 GHz and 1410–1910 GHz. In this paper, we report on the analysis of electrical standing waves that are present between the hot electron bolometer (HEB) heterodyne mixing element and the first low noise amplifier in the HIFI instrument. We show that the standing wave shape is not a standard sinusoid and difficult to remove from the resulting spectrum using standard fitting methods. We present a method to remove the standing waves based on data taken during the HIFI instrument level test, and anticipate the use of a similar calibration procedure in actual flight. Using the standing wave profile we obtain direct evidence of the complex IF output impedance of the HEB mixer.