Arthrospira is an edible cyanobacterium that contains valuable biomolecules, including proteins, carbohydrates, pigments, and β-glucans. This study aimed to determine the biochemical compositions of the two species of Arthrospira cultivated in anaerobic digestion effluent obtained from water hyacinth. This fast-growing aquatic macrophyte causes significant environmental issues worldwide. It’s an urgent issue to confirm the utility of such nuisance macrophyte for sustainable management of freshwater ecosystems. Even with six- and eight-fold diluted effluent containing a limited amount of phosphate, algal biomass production was 0.62 g/L, with higher carbohydrate but lower protein and lipid content than those in the algal cells cultivated with standard media. β-glucan was produced at 4–18% of algal dry mass, being 1.5–7 times higher than those in the standard media. Additionally, phosphate and ammonium removal efficiencies in the cultivation were over 96%. These findings suggest that cultivating Arthrospira using the effluent has promising potential for producing algal material including valuable biomolecules like β-glucans from nuisance macrophytes through sustainable nutrient recycling.