AbstractRecent advances in sorting flow cytometry (SFCM) and sensitive biochemical techniques have opened the door for a variety of new incubation‐free measurements to assess cell physiology. We adapted highly sensitive bioluminescent methodologies to measure cell NAD(H) and adenosine triphosphate (ATP) contents as predictors of phytoplankton primary production and growth rate. We first applied these methods to algae in taxonomically distinct groups: the chlorophyte Dunaliella tertiolecta, the diatom Thalassiosira pseudonana and a model cyanobacterium Synechococcus sp. WH8102. We found that NAD(H) content [NAD(H)phyto] increased significantly with increasing net primary productivity (NPP) and growth rate. In contrast, and in agreement with previous studies, phytoplankton ATP content (ATPphyto) was highly correlated with carbon biomass. Furthermore, ATPphyto was not correlated with NPP or growth rate. As a field test of the method, we then measured NAD(H)phyto in phytoplankton samples collected by SFCM in the North Pacific. These measurements yielded an estimate of NPP closely matching that from the traditional incubation‐dependent 14C uptake technique. The methods described here enable low‐biomass, incubation‐free estimates of phytoplankton NPP, growth rate, and biomass.