Increased seawater temperatures and nutrient loading are stressors that affect coral reefs and their microbiomes. In this study, filamentous algae were collected and exposed to different temperatures and nutrient concentrations through a laboratory experiment. Microbial DNA was extracted and analyzed using amplicon sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. In total, 1 domain, 51 phyla, 131 classes, 335 orders, 549 families, and 1905 species were identified. Proteobacteria and Bacteroidota were the dominant taxa reported. Elevated seawater temperatures and nutrient enrichment impacted microbial communities associated with turf algae under laboratory culture. Bacterial species diversity and abundance differed under different temperature and nutrient conditions. Proteobacteria and Actinobacteria were abundant in lower-temperature conditions, while Desulfobacterota, Spirochaetota, and Firmicutes were abundant in higher-temperature conditions. Ruegeria was abundant in low-temperature conditions, whereas Vibrio abundance was low. Regarding nutrient conditions, Proteobacteria and Cyanobacteria were abundant under high-nutrient conditions, while Firmicutes and Desulfobacterota were abundant under ambient-nutrient conditions. The higher nutrient concentration increased the abundance of pathogenic bacteria, such as Vibrio and Photobacterium, while Pseudoalteromonas, which is beneficial for reefs, was present under ambient nutrient conditions. This study demonstrates that temperature and nutrient enrichment can shape microbial communities under laboratory conditions, providing an experimental setting for further studies of bacterial functions and metabolic processes in natural conditions under thermal and nutrient stresses.