It is known that solvent and solvent effect play an important role in many catalytic reactions. Here the effect of water and water structure on acid catalyzed polysaccharide hydrolysis and monomer sugar conversion to furfural and HMF were investigated. Ab initio molecular dynamics and metadynamics simulations were used to investigate the energetics of several competing pathways encountered during dilute acid pretreatment. The multi-dimensional free energy surfaces (FES) obtained allows accurate determination of both the reaction free energies and barriers of these reaction processes. Water is found to play a critical role during proton catalyzed sugar reactions.  Water and water structure affect both the reaction pathways, reaction free energies and barriers significantly. The thermodynamic equilibrium and the kinetic reaction rate constants were also determined and compared with available experimental data.