Microplastic (MP) pollution is ubiquitous in the aquatic environment, with significant quantities of MPs originating from municipal wastewater treatment plants. Efforts to evaluate and implement MP removal processes are underway, with membrane technologies often recommended as an "ideal" solution. A key challenge in evaluating these technologies involves efficiently quantifying MP concentrations in samples. Here, flow cytometry (FC) is demonstrated as an effective technique to obtain concentration measurements of plastic microbeads (MBs; 1-5 μm) suspended in water with/without added humic acid. Regardless of solution conditions, MB concentrations were easily quantified via FC. Subsequently, two microfiltration membranes were challenged to these suspensions. As measured via FC, the 0.45 μm membrane demonstrated effective MB rejection (>99%) whereas the 5 μm membrane exhibited a broad range of rejections (40% to >95%) depending on solution conditions and filtration time. Finally, a model was formulated utilizing FC forward light scattering intensity measurements to estimate MB sizes in samples. Using the model, a 33% reduction in median MB size, on average, was noted across the 5 μm membrane when filtering MBs suspended in humic acid solution, affirming a preferential permeation of smaller particles. Overall, this study advances MP quantification techniques towards validating removal processes.