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In freshwater aquaculture ecosystems with high-frequency occurrences of cyanobacteria blooms, a chronic neurotoxic cyanobacteria toxin, β- N -methylamino- l -alanine (BMAA), is a new pollutant that affects the normal growth, development, and reproduction of aquaculture organisms. BMAA poses a great threat to the food quality and food safety of aquatic products. In this paper, high-performance liquid chromatography-mass spectrometry (HPLC-MS/MS) was used to detect the contents of BMAA in the edible portions of six representative freshwater aquaculture products (Corbicula fluminea, Anodonta arcaeformis, Macrobrachium nipponense, Eriocheir sinensis, Ctenopharyngodon idella, and Mylopharyngodon piceus) from Taihu Lake Basin in China. Noncarcinogenic health risks were assessed with reference to the model recommended by the International Environmental Modelling and Software Society and based on the biomagnification characteristics of BMAA in the various aquaculture products investigated by the stable nitrogen isotope technique. The average BMAA concentrations in the edible portions of the six freshwater culture products were from 2.05 ± 1.40 to 4.21 ± 1.26 μg g−1 dry weight (DW), and the difference was significant (p < 0.05), such a difference increased with the increase in the trophic level in the aquaculture products. Although a biomagnification indication was observed, the trophic magnification factor (TMF) was only 1.20 which exhibited a relatively low biomagnification efficiency. The annual health risk values of BMAA in all the measured aquatic products were within the maximum tolerable range (<1 × 10−6 a−1), and the health risk increased with the increase in the trophic level. The risk values of BMAA in the six freshwater aquaculture products for children was slightly higher than the negligible level (<1 × 10−7 a−1), thus there might have potential health risks for children's long-term consumption. Considering China's national conditions, the guidance values of BMAA based on the quality and safety of freshwater aquaculture products were proposed to be 7.2 μg g−1 DW for adults and 1.8 μg g−1 DW for children. Image 1 • BMAA in freshwater aquaculture products (FAPs) were investigated. • Biomagnification characteristics of BMAA in FAPs were revealed. • Noncarcinogenic health risks of BMAA in FAPs were assessed. • Guidance values of BMAA were proposed to ensure the quality and safety of FAPs. [ABSTRACT FROM AUTHOR]