The chemical nature of Si(100) and (111) surfaces during immersion in dilute hydrofluoric acid (HF) solution and water was investigated “in-situ” and in real time using infrared absorption spectroscopy in the multiple internal reflection geometry. We demonstrate that in dilute HF solution, Si surfaces are not perfectly terminated by hydrogen, but are covered in part with hydrogen-associated Si fluorides, such as SiH2(SiF). We find that the hydrogen coverage of the surface during storage in dilute HF solution depends on the HF concentration of the solution. It is shown that rinsing in water following HF treatment leads to complete hydrogen termination of the surface. We also show that hydrogen exchange reaction occurs on the hydrogen-terminated Si surface during storage in water.