Group IV nanowires synthesized via the vapor-liquid-solid (VLS) technique do not frequently exhibit planar defects and/or polytypic domains. Even in group III-V nanowires, where these structural motifs are common, rational control of their position remains challenging. Since defect energetics are similar in both systems, the observed structural differences are especially striking and indicate that the underlying physical phenomena are not sufficiently well understood. Here, we demonstrate how user-defined changes in surface chemistry near the triple-phase line can introduce twin planes and stacking faults during the growth of <111> oriented Si nanowires. More specifically, the addition of atomic hydrogen during Si nanowire growth enables {111} defects that begin at the <112> sidewall and continue to propagate across the nanowire even after the flux of atomic hydrogen ceases. Real-time in-situ infrared spectroscopy measurements reveal that covalent Si-H bonds are responsible for the defect initiation process and a simple mechanistic model will be presented to explain these results. Our findings are an important step toward a fundamental understanding of the chemistry that governs semiconductor nanowire synthesis and suggest a new route to engineer the properties of Si.