To evaluate the health risk of cyanobacterial blooms, the levels of the neurotoxic non-protein amino acid, β-methylamino-l-alanine (BMAA), was investigated in the freshwater ecosystem of Gonghu Bay in Lake Taihu. Lake Taihu is a large shallow lake contaminated by the excessive growth of Microcystis. Since BMAA has been measured in diverse cyanobacteria in different ecosystems all over the world, BMAA might also occur in Gonghu Bay. A long term monitoring of BMAA was done by HPLC-MS/MS method in cyanobacteria, mollusks, crustaceans and various fish species at different trophic levels of ecosystems in Gonghu Bay, some of which were popularly consumed by humans. Over the entire sampling period, the total average BMAA content in cyanobacteria, mollusks, crustaceans and various fish species were 4.12, 3.21, 3.76, and 6.05μgBMAA/g dry weight, respectively. Thus, BMAA could be biosynthesized by the blooming cyanobacteria in which Microcystis dominates. This toxin can be transferred through ascending trophic levels of the aquatic ecosystem in Gonghu Bay. The bioaccumulation of BMAA was observed in aquatic animals, especially in some fish species during the bloom-outbreak and bloom-decline phases. The discovery of the chronic neurotoxin BMAA in a large limnic ecosystem together with possible pathways of accumulation within major food webs deserves serious consideration due to its potential long-term risk to human health. © 2013.