Seagrass is used as both food and herbal medicine to treat various ailments, including fever, skin diseases, wounds, stomach issues, stingray poison, muscle pain, and as a sedative for babies. Its efficacy is attributed to the active compounds it contains, such as antifungal, antimicrobial, anti-inflammatory, anticancer, antiviral, antioxidant, and cytotoxic agents. Given its potential, it is important to explore the chemical composition of seagrass. Furthermore, the analysis of these compounds should consider the environmental and habitat differences within the waters of Aceh. This study aimed to investigate the effect of water quality on the chemical composition and antioxidant activity of seagrass. The research was conducted from June to August 2024 in Aceh waters, specifically in Pulau Banyak and Aceh Besar. Seagrass samples were selected based on the species with the highest abundance, which were also sufficient for the extraction process. The average total phenolic content was 144.61±55.28mg GAE/g, the average flavonoid content was 123.37±33.22mg QE/g, the average chlorophyll content was 29.70±18.75 mg/g, the average carotenoid content was 57.70±23.94 mg/g, and the average antioxidant activity was 83.09±41.79 IC μg/mL. PCA analysis revealed that total phenolics, flavonoids, and chlorophyll were the three most influential chemical components in seagrass species. The water quality parameters in Pulau Banyak and Aceh Besar showed that current velocity, dissolved oxygen (DO), salinity, and temperature were all within the standards required for seagrass survival. Plot analysis results indicated that phosphate played a significant role in seagrass growth in Pulau Banyak, while nitrate was more important in Aceh Besar.