Because of its technological importance, silicon oxidation has been studied intensely for decades; however, the disordered nature of the oxide makes these reactions notoriously difficult to understand. In this work, the oxidation reaction is coupled with a subsequent etching reaction, allowing oxidation to literally write an atomic-scale record of its reactivity into the etched surface — a record that can be read with scanning tunneling microscopy (STM) and decoded into site-specific reaction rates, and thus chemical understanding, with the aid of simulations and infrared spectroscopy. This record overturns the long-standing and much-applied mechanism for the aqueous oxidation of the technologically important face of silicon, Si(100), and shows that the unusually high reactivity of a previously unrecognized surface species leads to a self-propagating etching reaction that produces near-atomically flat Si(100) in a beaker at room-temperature — a long-standing technological goal. These findings show that, contrary to expectation, the low-temperature oxidation of Si(100) is a highly site-specific reaction and suggests strategies for functionalization by low-temperature, solution-based reactions.