Molybdenum (Mo) coated soda‐lime glass is a commonly used substrate for Cu(InGa)Se2 solar cells as it also acts as the sodium (Na) source, which improves the efficiency of these devices. In this work, we investigate how oxygen controls the segregation and accumulation of Na on the Mo surface. A direct relationship between the concentration of surface oxygen and the amount of Na accumulation is showed. Values for the surface segregation ratio and grain boundary diffusion coefficient for Na in Mo are obtained by fitting diffusion data at several temperatures to a model for grain boundary diffusion. The results of this model reveal that surface oxygen controls the Na saturation level through its effect on the surface segregation of Na. An activation energy for grain boundary diffusion of Na is estimated and is similar to that of MoO bond dissociation in MoO3 suggesting the involvement of this bond during Na transport. © 2014 American Institute of Chemical Engineers AIChE J, 60: 2365–2372, 2014