Biofilms are a health and operating issue in various fields, particularly in drip irrigation systems based on reclaimed water. To ensure the proper functioning of drip irrigation systems and save water, biofouling needs to be detected and quantified in drippers. Few studies have investigated the use of near infrared (NIR) spectroscopy for biofilm monitoring, particularly in the context of drip irrigation systems. A major challenge lies in the strong influence of water on NIR spectra, which complicates biofilm detection and analysis. This study assessed polarization spectroscopy as a new approach to detect biofilms in the presence of water and to discriminate between biofilms and the embedded insoluble elements. Samples were probed with near infrared polarized light to collect single and multi-scattered light separately. Principal component analysis of the spectra in the 1100-1300 nm region was used to distinguish spectra associated with water alone and with biofilm samples in water. Biofilms of a thickness of less than 100 µm could be detected in the presence of water. Partial least squares with discriminant analysis (PLS-DA) was used to discriminate biofilms, biofilms with kaolinite, and biofilms with calcium carbonate (all in the presence of water). The method achieved a discrimination accuracy of 96.4%, demonstrating strong potential for application in cases of biofilm-induced composite clogging. Thus, polarized light spectroscopy in the near infrared region proves effective overcoming the presence of water for detecting and discriminating biofilms. This approach holds promise for application across various fields where biofilm formation presents a challenge.