Chlorophyll-a (Chl- a ) is considered an indicator of phytoplankton biomass dynamically reflecting the growth of algae. Therefore, determination of Chl- a threshold is of vital importance to the health of aquatic ecosystems and drinking water security. This research is aimed to investigate the spatial and temporal distributions of Chl- a and microcystin (MC) concentrations using Geographic Information System (GIS) and identify the Chl- a threshold in Lake Taihu based on available guideline values of MCs. Nearly the same characteristics of spatiotemporal variation of Chl- a and MCs were observed in Lake Taihu. Overall, the lakewide distributions of Chl- a and MCs were highly variable over time and space. The Chl- a concentration in the winter and spring was relatively low, and gradually increasing in summer and autumn, with the maximum concentration observed in August. But the maximum MCs concentration appeared in October, two months lagging behind the Chl- a . The highest annual average Chl- a and MCs concentrations were observed in Zhushan Bay, Meiliang Bay, Gonghu Bay in northwest of Lake Taihu, following by West Zone and Center Zone. Dongtaihu Bay, East Zone and South Zone always present good water quality. Referring to the guideline value of MCs, the Chl- a threshold was determined as 10-15 mg·m -3 based on the linear regression correlation between Chl- a and MCs. The establishment of Chl- a threshold is useful for eutrophication control, water quality management and drinking water utilities in developing water safety plans.