The properties of materials confined in porous media are important in scientific and technological aspects. Topology, size, and surface polarity of the pores play a critical role in the confinement effects, however, knowledge regarding the guest-pore interface structure is still lacking. Herein, we show that the molecular mobility of water confined in periodic mesoporous organosilicas (PMOs) is influenced by the polarity of the organic moiety. Multidimensional solid-state NMR spectroscopy directly probes the spatial arrangement of water inside the pores, showing that water interacts either with only the silicate layer or with both silicate and organic layers depending on the alternating surface polarity. A modulated and a uniform pore filling mode are proposed for different types of PMOs.