Microplastics of millimeter dimensions have been widely investigated in environmental compartments and today, studies are mainly focused on particles of smaller dimensions (< 500 µm). However, as there are no relevant standards or policies for the preparation and analysis of complex water samples containing such particles, the results may be questionable. Therefore, a methodological approach for 10 µm to 500 µm microplastic analysis was developed using μ-FTIR spectroscopy coupled with the siMPle analytical software. This was undertaken on different water samples (sea, fresh, and wastewater) taking into consideration rinsing water, digestion protocols, collection of microplastics, and sample characteristics. Ultrapure water was the optimal rinsing water and ethanol was also proposed with a mandatory previous filtration. Although water quality could give some guidelines for the selection of digestion protocols, it is not the only decisive factor. The methodology approach by μ-FTIR spectroscopy was finally assessed to be effective and reliable. This improved quantitative and qualitative analytical methodology for microplastic detection can then be used to assess the removal efficiency of conventional and membrane treatment processes in different water treatment plants.