Methods and systems for watermarking of signals employ time frequency analysis. An encoding method divides the signal into segments, transforms each segment into a time-frequency representation, and computes a time-frequency domain watermark signal based on the time frequency representation. It then combines the time-frequency domain watermark signal with the media signal to produce a watermarked media signal. To embed a message using this method, one may use peak modulation, pseudorandom noise modulation, statistical feature modulation, etc. Watermarking that uses a time-frequency representation enables the encoder to adapt and or derive the modifications made to embed data based on the time frequency representation.