Individual cell growth rates enhance our understanding of microbial roles in regulating organic matter flux in marine and other aquatic systems. We devised a protocol to microscopically detect and quantify bacteria undergoing replication in seawater using the thymidine analog 5-ethynyl-2’-deoxyuridine (EdU), which becomes incorporated into bacterial DNA and is detected with a ‘click’chemistry reaction in< 1 h. Distinct EdU localization patterns were observed within individual labeled cells, eg some displayed 2 or more distinct EdU loci within a single DAPI-stained region, which likely indicated poleward migration of nascent DNA during the early phase of replication. Cell labeling ranged from 4.4 to 49%, comparable with cell labeling in parallel incubations for 3 H-thymidine microautoradiography. Meanwhile, EdU signal intensities in cells ranged> 3 orders of magnitude, wherein the most intensely labeled cells comprised most of a sample’s sum community EdU signal, eg 26% of cells comprised 80% of the sum signal. This ability to rapidly detect and quantify signals in labeled DNA is an important step toward a robust approach for the determination of single-cell growth rates in natural assemblages and for linking growth rates with microscale biogeochemical dynamics.