Low-micrometer microplastics (LMMPs), typically in the size range, 1–10 μm, are emerging contaminants ubiquitously present in aquatic systems. However, the quantification of LMMP mixtures in environmental waters is hindered by the limitations of current analytical methods. In this study, we developed a novel analytical method that couples a fractionated membrane filtration with Raman microspectroscopy (μ-Raman) to reliably quantify LMMPs in lake water. The fractionated membrane filtration system recovered >90% of the mixed polystyrene (PS) and poly(methyl methacrylate) (PMMA) LMMPs (i.e., 1.5, 3, 5, and 8 μm) from water. By separating LMMPs into 1–5 and 5–10 μm size fractions, the quality of the Raman images of small LMMPs (i.e., 1.5 and 3 μm particles) acquired directly on the membrane filters improved substantially. The reliability of LMMP Raman imaging was further improved by tracking the sum and product of their three characteristic Raman bands. In this way, the interferent Raman signals from the lake water matrix and membrane filters were significantly suppressed. This method provides a reliable tool to recover, separate, and quantify LMMP mixtures in complex water matrices, paving the way toward a deeper understanding of their environmental implications.