Microorganisms in membrane systems tend to adhere to surfaces and to form a gel layer called biofilm, which participates in the separation process as a secondary membrane. On the raw water side, it causes an increase of fluid friction resistance which increases Delta p(feed/brine). Also, overall hydraulic resistance of the membrane Delta p(membrane) Can increase due to the biofilm. If these effects exceed a certain threshold of interference, they are addressed as biofouling. Countermeasures require a three step protocol: (1) detection, (2) sanitation, and (3) prevention. Detection has to be performed on the surface as planctonic cell numbers released randomly from the biofilm do reflect neither site nor extent of biofilm growth. The analysis includes microbiological and biochemical parameters; the differentiation between other kinds of fouling such as scaling or organic fouling can be performed by FTIR-ATR spectroscopical analysis. Sanitation should be focused on removal of the biomass rather than on killing the microorganisms attached to the surface. First, the slime matrix, consisting mainly of polysaccharides and proteins, must be weakened. This requires interference with the binding forces, which are weak physico-chemical interactions such as hydrogen bonds, van der Waals and electrostatical interactions. Then, increased shear forces can remove the biomass. A preventive concept should acknowledge the fact that biodegradable substances in the water represent the biofouling potential. Biofouling can be regarded as a "biofilm reactor in the wrong place". Reduction of the nutrient content of the raw water can be achieved by a "biofilm reactor in the right place", i.e., a biofilter on which microorganisms form biofilms and sequester the nutrients from the water phase. Mandatory for any optimized antifouling strategy is monitoring of biofilm development; a fiber optical device which provides real-time, on-line, in situ information non-destructively is proposed which can be adjusted to membrane modules.