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Water levels in cryoconite holes were monitored at high resolution over a 3‐week period on Austre Brøggerbreen (Svalbard). These data were combined with melt and energy balance modelling, providing insights into the evolution of the glacier's near‐surface hydrology and confirming that the hydrology of the near‐surface, porous ice known as the ‘weathering crust’ is dynamic and analogous to a shallow‐perched aquifer. A positive correlation between radiative forcing of melt and drainage efficiency was found within the weathering crust. This likely resulted from diurnal contraction and dilation of interstitial pore spaces driven by variations in radiative and turbulent fluxes in the surface energy balance, occasionally causing ‘sudden drainage events’. A linear decrease in water levels in cryoconite holes was also observed and attributed to cumulative increases in near‐surface ice porosity over the measurement period. The transport of particulate matter and microbes between cryoconite holes through the porous weathering crust is shown to be dependent upon weathering crust hydraulics and particle size. Cryoconite holes therefore yield an indication of the hydrological dynamics of the weathering crust and provide long‐term storage loci for cryoconite at the glacier surface. This study highlights the importance of the weathering crust as a crucial component of the hydrology, ecology and biogeochemistry of the glacier ecosystem and glacierized regions and demonstrates the utility of cryoconite holes as natural piezometers on glacier surfaces.