Soil organic matter (SOM) is an important factor influencing aggregate stability. Interactions between SOM and soil structure are widely studied, although the subtle relationship between SOM content, pore size distribution and aggregate stability is not fully known. Here we investigate such a relationship by means of a long-term experiment established in 1962 in northeastern Italy, which considers different fertilizer practices (organic, mineral and mixed) applied to a continuous maize crop rotation. We measured wet stability of 1–2 mm aggregates subjected to different pretreatments. Both soil physical properties (such as pore size distribution and hydrophobicity) and chemical properties (soil organic and humic carbon content) affecting aggregate stability were considered. The chemical structure of humic substances was characterized by thermal and spectroscopic analyses (TG-DTA, DRIFT and 1H HR MAS NMR). The Pore-Cor network model was then applied to evaluate the contribution of hydrophobicity and porosity to aggregate wetting. Our study suggests that SOM and its humic fraction can affect aggregate wetting and consequently slaking by modifying the pore size distribution with a shift from micropores (5–30 µm) and mesopores (30–75 µm) to ultramicropores (0.1–5 µm); hydrophobicity was also increased as a result of different humic composition. Spectroscopic analysis showed that hydrophobic compounds were mostly associated with complex humic molecules. Models of fast wetting dynamics, however, suggest that the contribution that hydrophobicity makes to aggregate stability, especially to soils with large carbon inputs, may not be the most significant factor.