In this study, the application of photoacoustic spectroscopy (FT-IR/PAS) is proposed to investigate membrane fouling phenomena. Ultrafiltration membranes made of polyether sulfone (PES) in modules operated at different flow regimes (dead-end and cross-flow) were used in this paper. Solutions of water-soluble poly(acrylic acid) and suspensions of a natural red clay were used as model media during the filtration tests. The research performed involved the possibility of tracking the in-situ rate of membrane fouling during filtration of these two types of media. Moreover, the influence of the molecular weight of the separated particles on the intensity of the membrane blocking was studied. The results of the experiments showed that fouling phenomena progress for various types of media filtrated is characterized by different particle sizes and can be simply detected using photoacoustic spectroscopy. It was also noted that an increase in the molecular weight of the filtrated medium, e.g., poly(acrylic acid) from 30 to 250 kDa, increased the intensity of membrane blocking of 57 and 87% for membrane installation with dead-end and cross-flow regime, respectively. The performed studies demonstrated that FT-IR/PAS can be also used to assess the efficiency of the methods used for membrane cleaning. The obtained results were confirmed by two other methods: a radiotracer technique and scanning electron microscopy.