A novel approach was used with data from the Moderate Resolution Imaging Spectroradiometer (MODIS) to characterize the intense blooms of cyanobacteria (primarily Microcystis aeruginosa) in Taihu Lake, China's third largest freshwater lake. The approach involves first deriving a floating algae index (FAI) based on the medium-resolution (250 and 500 m) MODIS reflectance data at 645, 859, and 1240 nm after correction of the ozone/gaseous absorption and Rayleigh scattering effects and then objectively determining the FAI threshold value (−0.004) to separate the bloom and nonbloom waters. By definition, the term “bloom” or “floating algae” refers to bloom where cyanobacteria form floating scums on the water surface. The 9 year MODIS time series data showed bloom characteristics (annual occurrence frequency, timing, and duration) between 2000 and 2008. Assuming 25% area coverage as a gauge for significance, significant bloom events rarely occurred between 2000 and 2004 for the entire lake (excluding East Bay) or several lake segments (Northwest Lake, Southwest Lake, and Central Lake). In most lake segments, the annual frequency of significant blooms increased from 2000–2004 to 2006–2008, when they started earlier and had a longer duration. The year 2007 showed unique bloom characteristics due to conditions highly favorable for bloom development and proliferation. The results suggest that the long-term bloom patterns are driven by both nutrients and climatic factors. The multiyear series of consistent MODIS FAI data products provide baseline information to monitor the lake's bloom condition, one of the critical water quality indicators, on a weekly basis, as well as to evaluate its future water quality trends.