Climate change is altering local temperatures and resource availability of many ecosystems. We explore the impacts of these changes on the metabolism of phytoplankton, organisms that are crucial as the base of aquatic food webs and engines of aquatic biogeochemical cycling. Specifically, we investigate the metabolic responses of six freshwater phytoplankton species---representing green algae, diatoms, and cyanobacteria---to warming in combination with light, phosphorus, and nitrogen, the three most critical resources for phytoplankton. Using direct-infusion mass spectrometry, a high-throughput metabolomics approach, we identify interactive effects of temperature and resource availability on phytoplankton metabolism. We detect thousands of metabolites involved in key pathways, including amino acid, carbohydrate, and lipid metabolism. Our results show that resource limitation had a stronger effect on metabolism than temperature across all species. While each resource induced distinct metabolic changes, nitrogen and phosphorus limitation triggered more similar responses, whereas light limitation resulted in a unique metabolic profile. We also identified a core set of metabolic pathways involved in all responses, alongside resource-specific pathways. These findings provide mechanistic insights into how phytoplankton metabolically respond to key environmental drivers, enhancing our understanding of their responses to future climate conditions.