The vascular endothelial surface glycocalyx layer consists of fibrous glycoproteins with a thickness of several hundred nanometers to a few microns. The present study focuses on the function of the glycocalyx layer as a modulator of permeability in water transport across the blood vessel wall. A particulate layer model is developed to analyze the fluid permeation through the glycocalyx layer, which has periodic fibrous structures and finite thickness. Theoretical and numerical computations of the permeation resistance across the layer are performed based on the Stokesian dynamics approach. The results show that the resistance near the ends of the layer is affected considerably by the anisotropy of adjacent particle configurations. We describe such an end effect on the permeability in relation to the layer thickness and particle spacing ratio. It is suggested that the variations in thickness or fiber spacing in the glycocalyx layer could significantly alter its fluid permeation properties.