Microbial communities associated with benthic macroalgae play a central role in river ecosystem metabolism by mediating carbon and nutrient cycling, regulating nutrient availability, organic matter processing, and the transfer of energy to higher trophic levels. We studied how temperature affects microbial community composition, photosynthesis, and nitrogen fixation associated with the dominant filamentous green macroalga Cladophora glomerata in the South Fork Eel River, California. Cladophora often grows attached to the scoured bedrock and harbors a diverse epiphytic microbiome consisting of prokaryotic and eukaryotic taxa. In this nitrogen-limited river, the epiphyte assemblage often becomes dominated by Epithemia spp., diatoms with nitrogen-fixing endosymbionts that play a crucial role in the N budget of the river. To determine how temperature alters the microbial communities controlling nutrient cycling in Cladophora mats, we manipulated temperature in artificial flow-through stream mesocosms, maintaining three temperature treatments (ambient, +4 °C, +8 °C). We used stable isotopes of carbon (13C) and nitrogen (15N) to measure photosynthesis and nitrogen fixation. We analyzed changes in the microbial community using 18S and 16S rRNA amplicon sequencing. Results indicate that increasing temperature significantly altered both eukaryotic and prokaryotic communities, with a shift toward taxa commonly associated with decomposition, suggesting that warming may favor microbial assemblages linked to the breakdown of Cladophora biomass. Together, these results indicate that microbial assemblages associated with Cladophora respond to increasing temperature, while photosynthesis and nitrogen fixation rates remain unaffected across treatments.