Marine microbes mediate the vast majority of biological processes in the ocean. The transformation of inorganic carbon to organic carbon by photosynthetic microbes in the upper ocean supports the marine food web and is the first step in the process of carbon sequestration. The growth of photosynthetic microbes in most ocean waters around Australia is constrained by the availability of dissolved nitrogen, a macronutrient necessary for protein and nucleic acid synthesis. Nitrate reductase (NR) is one of the most important enzymes in the assimilation of exogenous nitrate. NR is associated with the cell membrane and is therefore an accessible target for conjugation with fluorescent antibodies, allowing quantification of changes in NR using flow cytometry. Functional shifts in the microbial community are typically measured in large volume (litres) bulk samples collected for molecular analyses. Here we demonstrate a new method targeting NR function of individual cells in small volumes (millilitres), resulting in deeper insight into marine microbial function.