A media thickness detection system for inkjet printing applications monitors the thickness of media entering the printer to ensure correct printing performance by adjusting the position of the printheads on-the-fly to assure printing quality. Media that do have an acceptable printing thickness are passed through the printer without stopping operation of the printer transport and without being printed upon and are routed directly to a reject facility. Embodiments also prevent damage to the printer by immediately stopping operation of the printer when substrate thickness deviates significantly from an expected value due to variations in thickness that result from manufacturing tolerances or damage to the substrate.