Understanding the mechanisms that control the filtration of a complex medium is a major challenge for the development of membrane-based processes in bio-industries, agro-industries or sludge treatment, where the complexity of the fluids is seen in terms of composition (liquid-liquid or liquid-solid mixtures), or physico-chemical characteristics (rheology, stability, etc.). This complexity is likely to induce different material organisations within the fluid depending on concentration and hydrodynamics fields. One of the aims of this study is to determine a relation between structural mechanisms and macroscopic properties of cakes formed on filtration of a colloidal suspension. Our investigations were carried out on clay suspensions. Filtration characteristics of those suspensions were investigated through simple dead end filtration tests and structural characteristics of the deposits formed during filtration were determined by using small-angle neutron scattering (SANS), static light scattering (SLS) and local birefringence techniques, associated with rheometric studies. These led to the conclusion that in the cakes formed from Laponite suspensions (volumic fraction=0.48%, transmembrane pressure=0.5 bar), the particles are packed in an anisotropic arrangement parallel to the membrane. Moreover, we show that upon filtration, an aggregation mechanism is promoted, leading to the formation of a porous fractal structure. This porous structure maintains some permeability in the cake. Adding a peptizer to the suspension changes the characteristics of the cake to a more regular ordering of the particle, with concentration fluctuations that have a lower fractal dimension. This ordered arrangement leads to a lower cake permeability.