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Water plays a fundamental role in the formation of planets and their atmospheres. Far-infrared observations with the Herschel Space Observatory revealed a surprisingly low abundance of cold-water reservoirs in protoplanetary discs. On the other hand, a handful of discs show emission of hot water transitions excited at temperatures above a few hundred Kelvin. In particular, the protoplanetary discs around the Herbig Ae stars HD 100546 and HD 163296 show opposite trends in terms of cold versus hot water emission: in the first case, the ground-state transitions are detected and the high-J lines are undetected, while the trend is opposite in HD 163296. As the different transitions arise from different regions of the disc, it is possible to address the overall distribution of water molecules throughout the disc. We performed a detailed spectral analysis using the thermo-chemical model DALI. We find that HD 163296 is characterised by a water-rich (abundance ≳10−5) hot inner disc (within the snow line) and a water-poor (40 au). The emitting region of the cold H2O transitions is spatially coincident with that of the H2O ice previously seen in the near-infrared. Notably, milµmetre observations with ALMA reveal the presence of a large dust gap between nearly 40 and 150 au, likely opened by a massive embedded protoplanet. In both discs, we find that the warm molecular layer in the outer region (beyond the snow line) is highly depleted of water molecules, implying an oxygen-poor chemical composition of the gas. We speculate that gas-phase oxygen in the outer disc is readily depleted and its distribution in the disc is tightly coupled to the dynamics of the dust grains