The objective of this study was to evaluate the long-term effect of compaction on the pore system at 0.5 m depth of a heavy clay soil in Jokioinen, Finland. Gas diffusion and air permeability measurements were combined with pycnometer-estimated air-filled pore volumes. We wanted to evaluate, to what extent the compaction affected the air flow pattern in the macropores. The combination of diffusive and advective gas transport characteristics was expected to enhance the ability to deduce how the soil pore system was affected. This included advective air flow measurements at a range of pneumatic pressure drops. Compaction at 50 cm depth was persistent 29 years after the compaction event. Compaction diminished the size of vertical macropores that served as arterial pores, while the volume and role of marginal pores branching from the arterial pores were diminished. Compacted soil had the significantly lowest volume of blocked pores not in contact to the surrounding atmosphere. For this clay-holding soil, the long-term compaction effect is interpreted as a serious reduction of the aeration potential of the bulk soil matrix in between the vertical, arterial pores. Our data indicate a high degree of anisotropy of (clay-holding) subsoil pores, and that state-of-the art models are not able to describe soil diffusivity for such soils. We suggest air permeability measurements at a range of pressure drops in combination with a regression method for estimating Darcy air permeability. Care should be taken in using the specific permeability as an indication of pore tortuosity in cases, where the dimensions of the soil pores are significantly different.