High density nanofluidic channels were successfully fabricated by a novel process, nicknamed as self-sealing process, for the detection of metal nanoparticles dispersed in water using color changes excited by polarized electromagnetic waves. The permittivities of aqueous solutions with various concentrations of metal nanoparticles were calculated by a corrected plasma model. Systematic simulations using finite difference time domain method were carried out in investigating the detection capabilities of the nanofluidic channels for silver, beryllium and copper nanoparticles in water. The pronounced color shifts indicates that the channels possess high sensitivity in the metal nanoparticles detection. The designed nanofluidic channels were then fabricated by a direct flood deposition of a silica film on a pre-replicated hydrogen silsesquioxan (HSQ) grating using electron beam lithography (EBL). The self-sealing technique possesses advantages in simplified processing, encapsulation free and potential of multi-layer nanochannels.