An exemplary sound processor included in a cochlear implant system used by a patient generates a spectral input signal representative of spectral energy contained within a frequency band of an audio signal presented to the patient. The sound processor determines whether a spectral energy level of the spectral input signal exceeds a predetermined system noise threshold that is based on a characterization of system noise generated by the cochlear implant system within the frequency band. The sound processer then generates a spectral output signal by 1) including the spectral input signal in the spectral output signal if the spectral energy level exceeds the predetermined system noise threshold, and 2) excluding the spectral input signal from the spectral output signal if the spectral energy level does not exceed the predetermined system noise threshold. Corresponding methods and systems are also disclosed.