Nutrition is at the center of interactions between organisms and their environment. During this time of unprecedented anthropogenic environmental change, biological indicators of nutritional changes and their effects on ecosystems are crucial if we are to understand and mitigate these changes. In this study, we developed a qPCR assay to examine nutritional responsiveness of ten genes identified as potential indicators of nutritional state in the freshwater zooplankton Daphnia pulex. We grew animals in six ecologically relevant treatments: nutrient replete, low carbon (food), low phosphorus, low nitrogen, low calcium, and high Cyanobacteria. We measured the growth rate and elemental composition of these animals and extracted their RNA. We then selected ten nutrient sensitive genes, two per limiting nutrient, and two reference genes from an RNA sequencing dataset of Daphnia pulex grown under the same six nutritional treatments. We then designed and validated qPCR primers for the ten indicator and two reference genes. We ran qPCR using these primers on cDNA from our experimental animals and found that the differential expression patterns of these genes could discriminate between our six nutritional states with high levels of accuracy. These results represent a compelling proof of concept for the use of gene-based nutritional biomarkers, paving the way for the use of genetically based nutritional state biomarkers in the study of ecology