The phenomenon of fouling of microfiltration membranes by much smaller particles such as proteins is described by a new developed simulation algorithm based on diffusion limited aggregation simulation techniques. The model specifies the membrane morphology explicitly and allows to (a) characterize the deposit morphology and (b) quantify the flux decline and the retention increase as a function of membrane morphology. Simulations suggest that the aggregate density above the pore opening is smaller than the aggregate density above the flat adsorption surface. The flux decline as a function of number of particles deposited shows two distinct regimes. Initially the flux decline is determined by internal fouling and membranes with the same initial flux but different pore diameter show different flux decline: the membrane with the smaller pore has a more rapid flux decline. Also, the effect of membrane thickness on flux decline and retention can be distinguished. The current model is compared with macroscopic models such as the pore blocking model, cake filtration model and the internal filtration model. Finally, the paper discusses the current limitations of the algorithm and points out opportunities for model improvement to further approach experimental reality.