One of the main obstacles impeding implementation of membrane distillation for the recovery and concentration of ammonia from swine manure is wetting caused by fouling. Due to the different types of fouling which can occur in a membrane system, foulants characterization is a complex problem. To elucidate the fouling mechanism, deposit morphology and composition of foulants have been determined using Scanning Electron Microscopy, X-ray Energy Dispersive Spectrometry, Attenuated Total Reflectance Infrared Spectrometry, Ion chromatography and Inductively coupled plasma-optical emission spectroscopy. Based on the analysis of fouled membranes, it is concluded that membrane fouling is dominated by organic fouling in combination with deposits of inorganic elements and microorganisms. After a week of running the membrane process without cleaning, the average fouling layer thickness was estimated to 10-15μm. The fouling layer further results in a loss of membrane hydrophobicity. This indicates that fouling could be a severe problem for membrane distillation performance.