The work demonstrated in this thesis represent the path towards developing the large-scale fabrication of two-dimensional nanoporous membrane devices and use thereof as platforms to study nanoscale physics of water and ion flow through confined channels. Methods developed here are used to fabricate molybdenum disulfide (MoS2) membrane devices and investigate the fundamental physics of nanopore systems and thin films in aqueous solutions. In particular, the second chapter presents the accomplishments in the large-area MoS2 synthesis via chemical vapor deposition. Process modifications such as the use of spin-coated precursors/growth promoters and addition of active gases such as H2O vapor or moderate amount of O2 enable to scale up the growth reaction into the synthesis of a continuous monolayer films on 2-, 3- and 4-inch substrates. Third chapter shows the application of focused ion beam irradiation for engineering, imaging and studying optically active defects in MoS2 and hexagonal boron nitride films. On top of that, the ion irradiation protocol was used for establishing the tunable and large-throughout nanopore drilling process on suspended MoS2 membranes. With the high-resolution, scanning electron transmission microscopy, nanopores were investigated with an analysis script and classified based on the pore geometries and edge composition. Coupled with molecular dynamics simulations the membranes populated with ~1nm nanopores were assessed in the context of emerging ion- and water- permeation properties. The last, fourth chapter presents the application of nanoporous membranes discussed in previous chapters in the nanofluidics study application. A particular emphasis is put on the application of hydrostatic pressure in nanopore experiments as an additional measurement probe. Experimental results shown in this chapter uncover the non-linear signals originating from nanobubbles pinning, improper wetting and membrane adhesion issues. With the assistance of hydrostatic pressure, the nanoporous MoS2 suspended membranes are then further investigated to explore the ion transport properties and nanopores behaviour under applied strain in the context of artificial mechanosensing as well as osmotic power generation in salinity gradients. The ion irradiated, atomically thin films proved to be a highly attractive membrane materials and demonstrated a great promise in broad nanofluidic applications. Insights acquired during the thesis study were used to advance the state-of-art knowledge in field of the synthesis and application of 2D membranes in the nanofluidics research.