Graphene oxide (GO) membranes have been reported to be a promising separation barrier that can retain small molecules and multi-valent salts because of the well-defined interlayer space between GO flakes. However, while some studies suggested fast liquid transport through the extremely tortuous transport path, contradictory observations (e.g. low permeation flux) have also been obtained. This paper revealed the dynamic microstructure of GO membranes, which affected the membrane performance significantly. We showed that all GO membranes prepared by varied methods and on different substrates presented a severe reduction in water permeability during filtration, due to the compaction of their original loose microstructure. The water flux could drop continuously from tens of LMH bar−1 to <0.1 LMH bar−1 after more than ten hours. This result demonstrated that the structure of GO membranes prepared by current approaches was far from the ideal laminar structure. The high permeability of GO membranes observed could be contributed by the disordered membrane microstructure. Therefore, the transport mechanisms assuming perfect laminar structure in GO membranes, and the fast transport hypothesis may not fully describe the water transport in GO membranes. Interestingly, the loosely packed microstructure of GO membranes was also found reversible depending on the storage conditions.