Water interaction and transport through nanochannels of two-dimensional (2D) nanomaterials hold great promises in several applications including separation, energy harvesting and drug delivery. However, the fundamental underpinning of the electronic phenomena at the interface of such systems is poorly understood. Inspired by recent experiments, herein, we focus on water/heavy water in boron nitride (BN) nanochannels – as a model system – and report a series of ab initio based density functional theory (DFT) calculations on correlating the stability of adsorption and interfacial properties, decoding various synergies in the complex interfacial interactions of water encapsulated in BN nanocapillaries. We provide a comparison of phonon vibrational modes of water and heavy water (D2O) captured in bilayer BN (BLBN) to compare their mobility and group speed as a key factor for separation mechanisms. This finding, combined with the fundamental insights into the nature of the interfacial properties, provides key hypotheses for the design of nanochannels.