Membranes are widely applied in water and waste water treatment as they provide an absolute barrier against the contaminants. Membranes are offered in wide pore size range and they are applied vastly due to their versatile and cost effective operation in dealing with wide range of streams. However, membranes, like any other filtration systems, suffer from fouling. Fouling layer, accumulation of rejected materials over time on membrane surface, is often called the main bottleneck of membrane processes. Fouling formation reduces water flux, increases energy consumption and leads to the early membrane replacement. To better control and mitigate fouling layer formation, better understanding of fouling mechanism and properties are required. Fouling properties can be categorized into hydraulic properties, mechanical properties, structural properties, chemical properties. These properties can be impacted by operational conditions, feed water quality and membrane properties. Moreover, these properties influence membrane performance parameters such as water flux, energy consumption and eventually the plant expenses. Therefore, the fouling properties, their inter-relations, their impacts on performance parameters should be further studied. We used novel modelling techniques and experimental measurements in laboratory and full-scale plants to study fouling properties and their impacts on membrane performance parameters. We also discussed the opportunities and challenges for future fouling study.Chapter 2. To evaluate the relation between structural, hydraulic and mechanical properties of fouling layer in the membrane systems, a novel method to extract these properties was developed to extracted fouling properties in a non-destructive and in-situ technique. The performance parameters of a dead-end UF system with integrated OCT imaging (in-situ) was coupled with a fully-coupled fluid-structural interaction (FSI) model. The dead-end UF was operated under a compression-relaxation cycle to evaluate how fouling properties changes under different applied pressure. Several mechanical models were evaluated to find the most suitable mechanical model to explain the fouling layer behaviour under compression-relaxation cycle in the dead-end UF. The results indicate that the hydraulic resistance of homogeneous biofilms under UF was much more affected by change in permeability than by the fouling layer thickness. Interestingly, we also found that even a poroelastic model (relatively simple model) can fairly good explain behaviour of the fouling layer in this study under different applied pressures. Compression of the fouling layer in UF systems can significantly increase hydraulic resistance of the membrane systems. In Chapter 2, a new technique was developed to extract fouling properties of the smooth surface biofilms. In Chapter 3 the new technique was further expanded to extract the mechanical properties of rough surface fouling layer under dead-end UF. We observed for the fouling layer which is fed with real surface water (i.e., river water), a dual-layer fouling structure with a thin and dense base layer and a thick and porous top layer could best explain the observed results. We also introduced a new fouling structure indicator, the fraction of exposed base layer, as a good indicator in the determination of water flux in UF systems.In Chapter 4 the chemical properties of fouling layer (e.g., composition) and their impacts on chemical cleaning efficiency in Reverse Osmosis (RO) systems were evaluated. Chemical cleaning protocols (often referred as CIP protocols) are usually developed under laboratory conditions (synthetic feed water, short-term experiments) and then are applied in the full-scale RO installations. This often leads to significant differences in CIP efficiency in the lab and full-scale installations. Thus, we compared the fouling layer properties and CIP efficiency of typical laboratory conditions RO and several full-scale RO plants. The results show that CIP efficiency in the full-scale RO plants are much lower than lab conditions RO. Later, we correlated such differences in CIP efficiency to their significantly different extracellular polymeric substance (EPS) properties. The EPS extracted from lab RO had different composition and adherence properties than the EPS extracted from full-scale RO. Therefore, we concluded that CIP protocols should not be developed under lab conditions. In the Chapter 5 we suggested a new method to better develop CIP protocols and study fouling properties with more industrial applications. We installed several new RO modules in the full-scale installation and they were operated for 30 days under identical conditions as the full-scale installation. Later, the fouling properties and CIP efficiency (in-situ measurement of permeability and pressure drop recovery) were compared between new RO modules (after 30 days of operation) and old RO modules (>2 years of operations). The new proposed fouling simulation method show promising results in both CIP efficiency results and fouling properties. Although fouling is inevitable part of filtration processes, its economic impacts on membrane systems is not well evaluated. In Chapter 6 cost of fouling in several RO and NF systems in The Netherlands has been calculated using plant performance data. All the cost factors contributing to cost of fouling such as CIP cost, energy cost, down cost were considered. We observed that for the RO plants, around a quarter of OPEX is caused by fouling, as oppose of around 10% for anoxic NF plants. The most important factor in the cost of fouling was considered the early membrane replacement cost, followed closely by additional energy cost. CIP costs have a minor contribution to the overall cost of fouling. Reuse of municipal wastewater effluent is part of solution to deal with water scarcity challenges. In Chapter 7 a fit-for-purpose approach to water reuse was proposed. We developed full techno-economic analysis on membrane-based Water reuse plant for municipal wastewater treatment effluent in the Netherlands. The impact of fouling and its properties and fouling cost have been integrated in all the membrane systems. A novel approach on design of water reuse plant has been offered to not only inherently reduce fouling impact but also increase plant robustness and water recovery. In chapter 8 a summarized and generalized conclusions of the previous chapters is presented. We also presents our suggestions and opportunities for the future membrane and fouling research.