Anaerobic membrane bioreactors (AnMBRs) offer a suitable alternative to existing lagoon and high-rate granular treatment options for high solids and fatty industrial wastewaters. AnMBR fouling is however, a major limitation to industrial applications, particularly in the treatment of complex, particulate substrate. Model analyses that integrate the multiple controlling factors of fouling offer a better understanding of controlling mechanisms than experimental analysis, however, existing membrane bioreactor (MBR) models are limited to simple hydraulic profiles and do not take into account complex reactor hydrodynamics. In response, this thesis investigated the effect of particulate fouling on AnMBR performance and identified the impact of reactor hydrodynamics on membrane fouling for the development of a holistic MBR optimisation model.Mechanistic fouling analysis identified that protein hydrophobicity and compressibility were key contributors to its high fouling propensity. Protein also showed high reactivity with lipids causing synergistic fouling behaviour in protein-lipid mixtures and a surfactant effect on lipids, changing the fouling mechanism from irreversible pore fouling in pure lipids to cake fouling in protein-lipid mixtures. CFD modelled shear was integrated into a distributed parameter model to simulate membrane fouling profile and flux distribution. Incorporation of a flux-pressure feedback loop allowed for the simulation of flux-step experiments and the prediction of critical flux. This model demonstrated a wide variety of applications including, for the identification of complex hollow fibre shear and the effect of operating conditions, such as total solids, sparge rate and filtration strategy, which can be directly applied to MBR design, optimisation and cost analyses.ii