In the present work we have evaluated the possibility of determining fat content in effluents produced by dairy plants using nylon membranes as a support for the retention of fat and registration of ATR IR spectra. Parameters that affect the sensitivity such as pore and diameter of the membranes, and sample volume have been optimized using powder and liquid milks of different origin and fat content. The possibility of applying this methodology under conditions of CIP processes has also been investigated. On the basis of the results obtained a new method is proposed for the quantification of fat at low mg/L levels. The utility of the method has been tested by analysing the effluents produced by a dairy pilot plant.