A method of chemical mechanical polishing includes bringing a substrate having a conductive layer disposed over a semiconductor wafer into contact with a polishing pad, generating relative motion between the substrate and the polishing pad, monitoring the substrate with an in-situ electromagnetic induction monitoring system as the conductive layer is polished to generate a sequence of signal values that depend on a thickness of the conductive layer, determining a sequence of thickness values for the conductive layer based on the sequence of signal values, and at least partially compensating for a contribution of conductivity of the semiconductor wafer to the signal values.