The aim of this study was to further understand the fouling and cleaning mechanisms of synthetic membranes used to filter an industrially relevant feed. The main focus of this study was to understand the fouling layer properties during pressure driven filtration. A relatively new technique known as Fluid Dynamic Gauging (FDG) was applied to examine the fouling layer thickness. This work comprised of four main themes with overlapping objectives: (i) the optimisation of Spent Sulphite Liquor fouling and cleaning conditions, (ii) the optimisation of molasses fouling and cleaning conditions, (iii) the investigation of the effect of a simple pre-treatment upon the membrane separation performance, and (iv) the application of the FDG in the study of polymeric membranes. An understanding of the mechanisms involved in fouling and cleaning of microfiltration and ultrafiltration membranes used to filter molasses and SSL has been attained. The variables affecting permeate flux and quality were optimised and mechanistic information concerning the synergistic effects between fouling and cleaning was gathered. The application of a simple NaOH pre-treatment was found to affect both the type of foulant species attaching to the membrane surface, and resulted in an altered separation and cleaning performance. Zeta potential measurements, FTIR and AFM demonstrated that both in-pore and surface fouling was present. The data collected indicated that for both membranes evaluated, different fouling species were found to have attached, depending upon the pre-treatment protocol used. These findings are significant, as they offer support to the recommendations made by some polymeric membrane manufacturers that conditioning protocols should include a NaOH step. However, in the SSL system examined, the effect of NaOH pre-treatment resulted in an improvement in the subsequent performance only over the first two or three complete filtration cycles. It is therefore necessary to study membrane systems over multiple fouling and cleaning cycles before a recommendation can be made. An improved understanding of the interaction between the surface chemistry and surface physics during membrane filtration of complex food based material will benefit both membrane manufactures and food industry based users. The technique of Fluid Dynamic Gauging was incorporated into an existing system and validated to monitor the development of cake layers over time. The FDG was also used to optimise conditions and track the thickness of the cake layer during multiple fouling cycles and its removal rate during cleaning, as an aid to understanding removal mechanisms. It has been shown that operating conditions have to be carefully chosen to minimise the effect of membrane fouling. The results show that FDG is a versatile and powerful technique for characterising the dynamics and mechanical behaviour of fouling layers on membrane surfaces. A particular advantage of the FDG technique is its ability to determine the thickness of fouling layers where other techniques would find difficulty. For example, the layers formed in this study were opaque, and consequently the determination of the development of deposit thickness with time would have been very challenging using conventional optical microscopy techniques.