Abstract Under ambient humidity, water spontaneously condenses in pores only a few nanometers in size, making nanoscale capillarity central to numerous natural phenomena and technological applications. At these dimensions, water may no longer be treated as a continuous fluid, yet the consequences of molecular discreteness for capillary condensation and filling remain poorly understood. Here we study two-dimensional (2D) nanocapillaries fabricated by van der Waals assembly and, using atomic force microscopy (AFM), monitor their wall deformations during humidity-driven water uptake. We observe two distinct regimes: layer-by-layer filling of flexible capillaries and abrupt filling of more rigid ones. Flexible walls deform in ≈3 Å steps, consistent with the entry of individual molecular layers of water. The different filling regimes are explained by a competition between wall deformation energy and oscillatory wall-water interactions. These results, together with the theoretical framework developed here, show how molecular discreteness can profoundly affect ubiquitous capillary phenomena, with wall rigidity determining whether this discreteness is exposed or hidden within an apparently classical, Kelvin-like response.