Accurate information on the interactions between water and silica is critical to the understanding of its properties including mechanical strength under stress and long-term chemical durability of silica and silicate glasses. In this study, interactions between water and nanoporous amorphous silica models were investigated using density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations which accurately describe bond breakage and formation as well as chemical reactions. AIMD simulations up to 30 ps were performed for systems containing water and nanoporous silica with a wide range of porosities (31%-67%). Partial removal of defects, such as two-membered rings, was observed during the AIMD runs whereas more reactive coordination defects were removed during the initial geometry optimization. The limited two-membered ring removal can be attributed to restricted water-defect movement or the increased stability of rings located on concave surfaces. Two-membered ring removal mechanisms included the formation of an overcoordinated silicon (Si-5) intermediate defect from the dynamic simulations. Si-5 defects continued to develop throughout the simulations, indicating a thermodynamic drive for two-membered ring removal which is kinetically limited. Changes in the electronic structures, such as atomic charges, and bond length-bond angle correlation functions were monitored during the hydroxylation process.