Global water scarcity fuels the search for innovative mitigation strategies for atmospheric water harvesting. Among these approaches, metal–organic frameworks (MOFs) have emerged as promising; however, the intricate atomic details and physical principles of the process of water adsorption are still unresolved. We deployed simulations to explore the mechanism of atmospheric water harvesting using MOF-303. Computer simulations reveal uptake capacity under varying humidity, mirroring the experiments. Molecular details afforded by simulations allow for the investigation of thermodynamic and dynamic factors governing the adsorption process. Our analysis revealed that the pyrazole group in the linker emerges as a pivotal water-binding site, enabling the nucleation of dense vapor to form unsaturated clusters. The unsaturated clusters formed inside the cavities were observed to grow to condense when removed from the framework, leading to facile release. This study elucidates the fundamental principles driving this process, guiding the enhanced design of materials for water harvesting.