Poor water quality is a global health concern affecting one billion people around the world. It is important to monitor water sources in order to maintain the quality of our drinking water and to avoid disease outbreaks. Targeting Escherichia coli as a faecal indicator is a widely used procedure, but the current methods are time consuming and not adequate to prevent spreading of faecal influence.   This Master thesis demonstrates the development of a near infrared fluorescence flow cytometer sensor system targeting Escherichia coli, using fluorescently labeled chicken IgY antibodies. The near infrared light was chosen to avoid fluorescence from blue-green algae that are present in the water source.   The hardware was developed with a 785  nm laser line to detect Alexa Fluor 790 labeled antibodies, using a photomultiplier tube or two different CMOS cameras. The antibodies were labeled using a commercial labeling kit, and evaluated using antibody binding assays and the developed hardware.   The IgY antibodies were successfully labeled with Alexa Fluor 790 and the function was maintained after the labeling process. The result demonstrates the principles of the sensor system and how it solved to the problem with fluorescence from blue-green algae. An aperture was used to overcome the suboptimal laser and filter setup, and to increase the sensitivity of the system. However, only a small fraction of the cells could be detected, due to challenges with the focal depth and loss of sensitivity in the photomultiplier tube at near infrared wavelengths. Further development is required to create a working product.