The adsorption and reactions of small molecules, such as water and oxygen, with graphene films is an area of active research, as graphene may hold the key to unique applications in electronics, batteries, and other technologies. Since the graphene films produced so far are typically polycrystalline, with point and line defects that can strongly affect gas adsorption, there is a need to understand their reactivity with environmentally abundant molecules that can adsorb and alter their properties. Here we report a study of the adsorption and reactions of water, oxygen, hydrogen, and ammonia on epitaxial graphene grown on Ru and Cu substrates using scanning tunneling microscopy (STM). We found that on Ru(0001) graphene line defects are extremely fragile toward chemical attack by water, which splits the graphene film into numerous fragments at temperatures as low as 90 K, followed by water intercalation under the graphene. On Cu(111) water can also split graphene but far less effectively, indicating that the chemical nature of the substrate strongly affects the reactivity of the C-C bonds in epitaxial graphene. Interestingly, no such effects were observed with other molecules, including oxygen, hydrogen, and ammonia also studied here.