Arcellinida are an established group of bioindicators in lake studies, but conventional labor-intensive microscopic analysis can limit the number of samples analysed. In this study, the FlowCam with VisualSpreadsheet (FCVS), a flow cytometer and microscope with machine learning software, was assessed as an instrument for rapid Arcellinida analysis. In a 2016 study, conventional Arcellinida analysis was performed on 46 samples collected from Wightman Cove, Oromocto Lake, New Brunswick, Canada. The samples were reanalyzed by FCVS and the two datasets were compared at the morphotype level using cluster and Bray-Curtis dissimilarity analyses. The methods produced highly similar arcellinidan assemblages that corresponded to specific lake habitats. FCVS was found to reduce analytical time by approximately 45%. FCVS shows potential as a reliable method for more rapid analysis of lacustrine Arcellinida; however, assemblage results can only be obtained at the morphotype level. Microscopic methods should still be used if species-level results are desired.