It is known that network modifying ions (such as alkali or alkaline earth ions) make glasses susceptible to aqueous corrosion, resulting in the alteration of their surface layers. However, the effect of the altered layers on the mechanical properties of glasses has not been well understood. In this work we study this effect using the pharmaceutical boroaluminosilicate (BAS) glasses as objects by performing nano- and macroscale mechanical tests. The results show that extending the corrosion time increases the thickness of the alteration layer of the BAS glass. The water-related species in the alteration layer lowers the nanohardness, the reduced modulus, the nanowear resistance and Vickers hardness. The corrosion-induced “silica-like” structure in alteration layer benefits the densification of the subsurface caused by nanoindentation and nanowear, and thereby enhances the fracture toughness of the BAS glass. The correlation between the water content in the alteration layer and the mechanical properties has been revealed. This work is instrumental in the design of the next generation of pharmaceutical glasses with higher toughness.