Nostoc sphaeroides (N. sphaeroides) is a commercially cultivated cyanobacterium, its flocculation activity has remained entirely unexplored. Here, we report the first systematic investigation of the flocculation performance, underlying mechanisms, and key influencing factors of N. sphaeroides homogenates against toxigenic Microcystis aeruginosa 7806 (M. aeruginosa) and natural water samples. Using kaolin as a test suspension, a flocculation efficiency of 91.7% was achieved under optimized conditions (0.5 g/L homogenate, 5 mmol/L CaCl2, and 50 min reaction time). The bioactive components were predominantly water-soluble extracellular polymeric substances, comprising 92.9% polysaccharides and only 1.8% proteins, identifying extracellular polysaccharides as the principal functional moiety driving flocculation. Calcium ions markedly enhanced flocculation via an adsorption-bridging mechanism, corroborated by a dose-dependent increase in calcium-binding capacity. The homogenate retained high flocculating activity across a temperature range of 30-90 °C, with optimal performance at pH 8.0, and multivalent cations (Ca2+, Mg2+, Fe3+) acted as superior coagulant aids compared to monovalent counterparts. Notably, post-flocculation, the Fv/Fm ratio and cellular surface integrity of M. aeruginosa remained intact, whereas extracellular microcystin concentrations in the culture medium declined substantially. This indicates that the flocculation process does not immediately compromise cell viability while effectively mitigating toxin-associated risks. In preliminary field trials with natural water, turbidity removal reached 47.9%, accompanied by measurable reductions in total nitrogen, total phosphorus, and ammonia nitrogen. Collectively, these findings establish, for the first time, that N. sphaeroides possesses both high flocculation efficiency and nutrient-removal capacity, positioning it as a promising, environmentally benign bioflocculant for natural water remediation.