Key TakeawaysFlow imaging microscopy (FIM) combines a flow cytometer's fluidic architecture with a microscope's spatial resolution to allow morphometric analysis of objects in suspensions such as water.FIM's real‐time analysis and identification of potential cyanotoxin producers help utilities understand population dynamics to maintain healthier source waters and reduce response times when a bloom is indicated.Case studies show FIM's advantages and limitations in harmful algal bloom monitoring programs for reservoir management and water treatment.