Unicellular plankton form the foundation of the marine food web, driving carbon fixation and cycling essential biogeochemical elements in marine ecosystems. Carbon biomass, often measured as a bulk property, serves as a common "currency" for ecologists. The increasing availability of metatranscriptomic data presents an opportunity to add taxonomic and functional resolution to ecological models and yet, aligning transcript counts with carbon biomass estimates remains a challenge. Here, we combine 30 quantitative metatranscriptome samples with Imaging FlowCytobot-derived carbon biomass estimates and demonstrate a robust, proportional (log-log scale) relationship between transcript concentration and carbon biomass estimates across abundant protist taxa. Further, we show that dinoflagellates exhibit a transcript-to-biomass ratio ~ 6.4-fold higher than other protist groups, consistent with their known transcriptional divergence. These findings provide a means to address overrepresentation of dinoflagellate transcript levels in metatranscriptome data. Moreover, this study establishes an entrée for integrating metatranscriptomics into carbon biomass-based ecological models, enhancing the interpretability and applicability of transcriptomic data in ecosystem research and modeling.