Consistent adsorption characterization of metal-organic frameworks (MOFs) is imperative for their wider adoption in industry and practical applications. Current approaches are based on the conventional intuitive representation of MOF pore space as a regular network of pore compartments (cages and channels), adsorption in which occurs independently according to their geometric dimensions. Here, we demonstrate that this conventional approach is unable to describe even qualitatively the shape of Ar adsorption isotherms on hydrated and dehydrated Cu-BTC structures, one of the most well-known MOF materials. A combination of geometric characterization of MOF crystallographic structure, molecular simulation, and virtual visualization of the adsorption process reveals that the filling of the adjacent pore compartments proceeds in parallel in a complex cooperative fashion. The proposed synergistic approach helps us to understand the relations between pore structure geometric and chemical features and adsorption behavior, laying down a foundation for improved methods for MOF characterization.