Cake growth during a low pressure cross-flow microfiltration (MF) of a Kraft lignin suspension was studied using fluid dynamic gauging (FDG). This is the first paper to discuss the identification of fouling mechanisms and their transition points based on simultaneous, in situ and in real-time FDG measurements of cake layer thickness and flux. The FDG results were used to quantify the significance of membrane pore-level fouling phenomena which occur at an early stage of the filtration. A flux decline of approximately 75% was attributed to membrane pore fouling i.e. deposition on the surface of the membrane which caused direct blocking of the membrane pores. We present here a novel toolset for quick and achievable diagnosis of membrane fouling mechanisms, which can accelerate innovations in membrane technology and process optimisation. Furthermore, this innovative approach showed good agreement with a mathematical approach, based on a critical flux model, which was applied to raw flux data. In addition to cake thickness measurements, destructive strength testing of the fouling layer showed an increase in cohesive strength over time. The results showed that filter cakes formed by Kraft lignin become harder to remove by shear stress as they become thicker during the course of the filtration. A removal mechanism for lignin layer under stress is also proposed. The methodology described here can be applied to rapidly predict and assess routes to performance improvements in cross-flow MF.