Soil structure refers to the way ultimate soil particles (i.e. clay, silt and sand) are arranged and bound together into groupings called aggregates or peds. The exchangeable cation of calcium, can initiate aggregation of these particles in a process called flocculation.

Flocculation occurs because the two positive charges of the calcium ion can attach to two separate and negatively charged clay mineral particle or organic colloid surfaces. This is similarly the case for aluminium. These cations effectively neutralize the negative surface charges.

The process of flocculation alone, however, does not make aggregates stable. Various soil satabilising agents are also necessary for the particles to aggregate.

This includes the presence of clay minerals, sesquioxides (i.e. aluminium- and iron-oxides) and humus. In the first instance, the negatively charged clay mineral surfaces can interact with each other and with sand and silt sized particles to form aggregates.

In addition, oxides of iron also link particles because some having positive charges, while other oxides have no charge but can build up tough coatings that connect particles.

Finally, large organic molecules tend to form bridges between mineral particles, either with electrostatic charge or by linking particles together like a net. Soil microorganisms provide the best cement because as they break down soil residues they produce gums that glue peds together.

These stabilizing agents along with the processes of localised compression resulting from repeated cycles of soil wetting and drying, shrinking and swelling and the action of organisms (flora and fauna) result in the repeated compression of the same soil mass. This leads to the increased coherence of aggregates (peds) that are difficult to pull apart.

The result is a well aggregated soil which contains large cracks or voids between the aggregated soil particles. These larger voids or macropores improve water infiltration, gaseous exchange and root penetration.