We studied how nutrient enrichment and increasing temperature affect algal species composition, photosynthesis, and nitrogen fixation using Cladophora glomerata and its epiphytes as a model system. The epiphyte assemblage of Cladophora in the Eel River, CA (a nitrogen limited system) experiences seasonal variability and becomes dominated by Epithemia spp., diatoms with a nitrogen fixing endosymbiont. We manipulated temperature and nutrients in artificial flow-through stream mesocosms where we maintained three temperature treatments (ambient, +4°C, +8°C) and three nutrient regimes (ambient, +nitrogen, +phosphorus). We analyzed eukaryotic species composition using next-generation sequencing and verified results with microscopy. We used stable isotopes of carbon (13C-CO2) and nitrogen (15N-N2) to measure photosynthesis and nitrogen fixation. Results indicate that neither photosynthesis nor nitrogen fixation were affected by temperature alone. In contrast, nutrient enrichment affected both processes. Both nitrogen and phosphorus stimulated photosynthesis, but the effect was most prominent under ambient temperature. Nitrogen enrichment strongly reduced nitrogen fixation across all temperature treatments. Phosphorus enrichment increased nitrogen fixation only at ambient and +4°C treatment but had no effect at the +8°C treatment. Together, these results indicate that ecosystem processes in this system are more sensitive to nutrient enrichment than temperature.