Although the positions of water guests in porous crystals can be identified, determination of their filling sequence remains challenging. We deciphered the water-filling mechanism for the state-of-the-art water-harvesting metal-organic framework MOF-303 by performing an extensive series of single-crystal x-ray diffraction measurements and density functional theory calculations. The first water molecules strongly bind to the polar organic linkers; they are followed by additional water molecules forming isolated clusters, then chains of clusters, and finally a water network. This evolution of water structures led us to modify the pores by the multivariate approach, thereby precisely modulating the binding strength of the first water molecules and deliberately shaping the water uptake behavior. This resulted in higher water productivity, as well as tunability of regeneration temperature and enthalpy, without compromising capacity and stability.