Nanochannels with nanoscale characteristic dimensions have sparked broad interest across scientific and engineering disciplines. The emergence of a versatile family of two-dimensional (2D) materials enables high-throughput engineering of nanochannels with tunable layered structural and functional properties in the form of laminar membranes, which opens up new opportunities for applications in liquid molecular separation, gas separation, and ion sieving. Despite significant progress in 2D-material-based nanochannel, thorough understanding of this field is still lacking. In this thesis, I systematically and in-depth explored the mechanism of nanochannel modification on filtration. I also fabricated a series of 2D-material-based nanochannel membranes for water treatment. My research demonstrated that interlayer spacing plays a crucial role in determining the selectivity and permeability of nanofiltration membranes. Proper tuning gives these membranes high throughput, precise selectivity, and multiple uses. [...]