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The structure and transport properties of alginate/chitosan microparticle membranes used in ethanol dehydration processes were investigated. The membranes were characterized based on images obtained from high-resolution microscopy. The following parameters were determined: the observed total amount of void space, the average size of the void domains, their length and diameter, the fractal dimension, and the generalized stochastic fractal parameters. The total amount of void space was determined to be between 54% and 64%. The average size of the void domains is smaller for alginate membranes containing neat (CS) and phosphorylated (CS-P) chitosan particles when compared to those membranes filled with glycidol-modified (CS-G) and glutaraldehyde crosslinked (CS-GA) chitosan particles. Furthermore, the transport of ethanol and water particles through the studied membranes was modelled using a random walk framework. It was observed that the results from the theoretical and experimental studies are directly correlated. The smallest values of water to ethanol diffusion coefficient ratios (i.e., 14) were obtained for Alg (sodium alginate) membranes loaded with the CS and CS-P particles, respectively. Significantly larger values (27 and 19) were noted for membranes filled with CS-G and CS-GA particles, respectively. The simulation results show that the size of channels which develop in the alginate matrix is less suited for ethanol molecules compared to water molecules because of their larger size. Such a situation facilitates the separation of water from ethanol. The comparison of the structural analysis of the membranes and random walk simulations allows one to understand the factors that influence the transport phenomena, in the studied membranes, and comment on the effect of the length, diameter, number of channels, and variations in the pore diameters on these transport parameters.