In the present study it is observed that alternate patterning of charged and neutral stripes on the surface of the graphene nanochannel lowers the water permeance and electro-osmotic flow velocity. However, for any charge configurations water permeance and electro-osmotic velocity through the nanochannel increase as surface charge density (σ) increases from 0.005 Cm^−2 to 0.025 Cm^−2 . With the further increase in σ, water permeance and electro-osmotic velocity through the nanochannel gradually decrease. Here factors like number of counter ions near the surface of the nanochannel, specific interactions between the wall and the water molecule/ion species play significant role in determining the flow behavior. These factors also influence the slip velocity of water molecules near the surface.