Water transport through graphene-derived membranes has gained much interest recently due to its promising potential in filtration and separation applications. In this work, we explore water permeation in graphene oxide membranes using atomistic simulations, by considering flow through interlayer gallery, expanded pores such as wrinkles of interedge spaces, and pores within the sheet. We find that although flow enhancement can be established by nanoconfinement, fast water transport through pristine graphene channels is prohibited by a prominent side-pinning effect from capillaries formed between oxidized regions. We then discuss flow enhancement in situations according to several recent experiments. These understandings are finally integrated into a complete picture to understand water permeation through the layer-by-layer and porous microstructure and could guide rational design of functional membranes for energy and environmental applications.