Models of Jupiter's formation and structure predict that its atmosphere is enriched in oxygen, relative to the Sun, and that consequently water clouds should be present globally near the 5-bar pressure level. Past attempts to confirm these predictions have led to contradictory results; in particular, the Galileo probe revealed a very dry atmosphere at the entry site, with no significant clouds at depths exceeding the 2-bar level. Although the entry site was known to be relatively cloud-free, the contrast between the observed local dryness and the expected global wetness was surprising. Here we analyse near-infrared (around 5 microm) observations of Jupiter, a spectral region that can reveal the water vapour abundance and vertical cloud structure in the troposphere. We find that humid and extremely dry regions exist in close proximity, and that some humid regions are spatially correlated with bright convective clouds extending from the deep water clouds to the visible atmosphere.