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The effect of non-idealities, namely pinhole defects and non-ideal lamellar stacking of nanosheets, on the performance of size-differentiated graphene oxide (GO) laminates is investigated using equilibrium molecular dynamics (MD) simulations. With the increase in sizes of the constituent GO nanosheets the water permeability of the layered GO membranes decreases and salt rejection increases. But with the inclusion of non-idealities the difference in water permeability between these membranes substantially reduced. The pinholes on the GO nanosheets provide shorter routes for trans-sheet flow, thereby increasing the water permeability of the membranes. The non-ideal stacking of the nanosheets without pinhole defects results in slight reduction in water permeability because of blockage of permeation pathways inside the membranes. However, with pinhole defects non-ideal stacking becomes favorable for water permeation through the layered GO membranes; as this time the non-ideal stacking leads to formation of voids inside the membranes, which act as routes for shorter permeation pathways. The effect of these non-idealities is more significant for layered GO membranes composed of large GO nanosheets. Although the water permeability through the layered GO membrane is greatly enhanced because of these non-idealities (about 10 times), the corresponding variation in the salt rejection is very low (