Marine bacterial and archaeal communities control global biogeochemical cycles through nutrient acquisition processes that are ultimately dictated by the metabolic requirements of individual cells. Currently lacking, however, is a sensitive, quick, and quantitative measurement of activity in these single cells. We tested the applicability of copper (I)-catalyzed cycloaddition, or click, chemistry to observe and estimate single-cell protein synthesis activity in natural assemblages and isolates of heterotrophic marine bacteria. Incorporation rates of the non-canonical methionine bioortholog L-homopropargylglycine (HPG) were quantified within individual cells by measuring fluorescence of alkyne-conjugated Alexa Fluor® 488 using epifluorescence microscopy. The method’s high sensitivity, along with a conversion factor derived from two Alteromonas spp. Isolates, revealed a broad range of cell-specific protein synthesis within natural microbial populations. Comparison with 35S-methionine microautoradiography showed that a large fraction of the natural marine bacterial assemblage (15-100%), previously considered inactive by autoradiography, were actively synthesizing protein. Data pooled from a large number of samples showed that cell-specific activity scaled logarithmically with cell volume. Assemblage activity distributions of each sample were fit to power-law functions, providing an illustrative and quantitative comparison of assemblages that demonstrate individual protein synthesis rates were commonly partitioned between cells in low- and high-metabolic states in our samples. The HPG method offers a simple potential approach to link individual cell physiology to the ecology and biogeochemistry of bacterial (micro)environments in the ocean.