Clay‐rich deposits are commonly assumed to be aquitards which act as natural hydraulic barriers due to their low hydraulic connectivity. Postdepositional weathering processes are known to increase the permeability of aquitards in the near surface but not impact on deeper parts of relatively thick formations. However, syndepositional processes affecting the hydraulic properties of aquitards have previously received little attention in the literature. Here, we analyze a 31 m deep sediment core recovered from an inland clay‐rich sedimentary sequence using a combination of techniques including particle size distribution and microscopy, centrifuge dye tracer testing and micro X‐ray CT imaging. Subaerial deposition of soils within these fine grained alluvial deposits has led to the preservation of considerable macropores (root channels or animal burrows). Connected pores and macropores thus account for vertical hydraulic conductivity (K) of
4.2×10−9 m/s (geometric mean of 13 samples) throughout the thick aquitard, compared to a matrix K that is likely <
10−10 m/s, the minimum K value that was measured. Our testing demonstrates that such syndepositional features may compromise the hydraulic integrity of what otherwise appears to have the characteristics of a much lower permeability aquitard. Heterogeneity within a clay‐rich matrix could also enhance vertical connectivity, as indicated by digital analysis of pore morphology in CT images. We highlight that the paleo‐environment under which the sediment was deposited must be considered when aquitards are investigated as potential natural hydraulic barriers and illustrate the value of combining multiple investigation techniques for characterizing clay‐rich deposits.