A method includes receiving (i) a plurality of electrocardiogram (ECG) signals acquired by a mapping catheter at a plurality of locations on a surface of a heart of a patient, (ii) a reference ECG signal from a reference catheter positioned at a nominal location in a coronary sinus (CS) of the patient, and (iii) position signals indicative of a position of the reference catheter in the CS. An electrophysiological (EP) map of at least part of the heart is calculated by time-referencing the ECG signals relative to the reference ECG signal. Based on the position signals, a displacement of the reference catheter from the nominal location in the CS, which distorts the time-referencing, is estimated. The distortion in the EP map is mitigated using the estimated displacement.