Reverse osmosis (RO) membrane technologies are essential to energy-saving and environmentally friendly desalination. While the separation mechanism is known to rely on cross-linked polyamide layers with subnanometer pores acting as selective barriers, the detailed structure of the water-transport channels within these pores remains poorly understood. This study revealed the molecular-level structure of water channels in polyamide pores using in situ X-ray absorption and X-ray emission spectroscopy. Our findings demonstrate that water molecules within polyamide pores possess different characteristics than those of bulk water, including a lower average coordination number of hydrogen bonds and distorted hydrogen-bonded structures. These structural features indicated to arise from the spatial constraints imposed by the surrounding polyamides in small pores. These water molecules are suggested to form interconnected clusters in large pores and contribute to selective permeability. Most significantly, we provide direct spectroscopic evidence for the local hydrogen bond structure of water, which has critical implications for optimizing RO membrane design. This molecular-level understanding of water hydrogen bond structure in the membrane pores creates new possibilities for enhancing membrane performance through targeted pore structure modifications.