Water, the elixir of life, faces a pressing challenge—salinity. As humanity's demand for freshwater intensifies, the significance of efficient desalination processes becomes paramount. The promising prospects of nanofluidic membranes and unique electrokinetic phenomena like ion concentration polarization (ICP) signal optimistic strides in enhancing salt removal processes. This study is dedicated to elucidating the transport mechanism of buffer ions at interfaces between micro and nanochannels. To achieve this, we introduce a multiphysics coupling model that incorporates a boundary condition for the fixed surface voltage, offering a comprehensive description of the impact of nanochannel arrays. In this context, it is important to note that the nanochannel array is characterized by a positive charge density, akin to a cation exchange membrane (CEM), seamlessly integrated into the microchannel wall to serve as a cationic half-cell. The analysis involved solving governing equations, including the Poisson-Nernst-Planck, continuity, and Navier-Stokes equations, numerically using the finite element method in an unsteady state. Employing cylindrical nanochannel array configurations—single, dual, and triple—we scrutinized their impact on salt species concentration and removal efficiency under specified conditions (c0=1mM, ρv=2C/m3, LN=10μm, VT=26mV, Vsurr=4VT, VL/VR=8,t≥0.5 and ζ=−60mV). The single nanochannel array configuration demonstrated a relatively uniform salt distribution, achieving a removal efficiency of approximately 58%. The introduction of two nanochannel arrays at distinct locations resulted in a notable increase in removal efficiency, reaching 72%, particularly in the "down first" configuration, emphasizing a synergistic effect. The presence of three nanochannel arrays, each with varying lengths, produced intricate patterns, with the highest removal efficiency observed at 91% in the "different length" condition. This study emphasizes the superior desalination capabilities achievable through multiple nanochannel arrays, advancing our understanding of nanofluidic membrane applications for efficient water desalination. In conclusion, emulating electrodialysis membrane procedures, particularly by integrating an anionic half-cell, holds promise for further advancing desalination processes, offering a potential avenue to enhance efficiency.