Hydrogen (H) released during the annealing of hydrogenated amorphous silicon nitride (SiNx:H) films diffuses through the crystalline silicon and passivates the defects. This study shows that the stable H isotope deuterium (D), which is released during the annealing of deuterated amorphous silicon nitride (SiNx:D) films, diffuses through the crystalline silicon and is subsequently captured by a thin, highly defective amorphous layer of silicon (a-Si) sputtered on the rear surface. We report on the measurement of the concentration of “penetrated” deuterium (hydrogen), by secondary ion mass spectrometry (SIMS) to monitor the flux of D diffusing through a defect-free single-crystalline silicon wafer. The penetrated D content in the trapping layer increases with the annealing time. However, the flux of D injected into the silicon from the SiNx layer decreases as annealing time increases. At an annealing temperature of 750 °C, D was found to penetrate through a 575 μm thick wafer in as little as 1 second peak annealing time in a Rapid Thermal Processing (RTP) system. Lifetime measurements on defective Si show that higher flux of H during the short RTP anneal is crucial for enhanced hydrogenation of the defects in Si.