The impact of pore size and pore surface composition on water dynamics confined in highly ordered porous silica material (MCM-41) was investigated using neutron scattering for correlation times in the picosecond range. Samples were synthesized by the hydrothermal route and grafted via the hydrolytic surface sol–gel method to obtain pore wall surfaces with Si–OH, Al–OH, or Zr–OH terminations and pore sizes from 2 to 2.7 nm. The samples were characterized after grafting using nitrogen adsorption–desorption isotherms and small-angle X-ray scattering. At room temperature, the analysis of the quasi-elastic neutron scattering data shows a decrease of mean square displacement of the mobile protons with the pore size and when Si–OH surface termination is replaced by Al–OH and Zr–OH. The water translational diffusion coefficients are close to the bulk value whatever the samples. The amounts of fixed protons depend on the pore size and the ability of the grafted layers to immobilize the water molecules which were determined also from thermogravimetric and differential thermal analysis. This last result highlights that pore surface composition could be the predominant parameter affecting the fixed proton content at this time scale.