Understanding the mechanisms that control the filtration of a complex media is a major challenge for the development of membrane-based processes in bioindustries, 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,..). This complexity is likely to induce different material organisation 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 clays suspensions. Filterability of those suspensions was appreciated throught simple dead en 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 anisotropical 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. Adding a peptiser to the suspension changes the structural characteristics of the cake in the sense of a higher fractal dimension in the arrangement. Macroscopic measurements of permeation velocity through the cakes formed with an without a peptiser showed that the initial aggregated state promoted by addition of a peptiser led in this case to a greater permeability.