A long-term satellite-based analysis was performed to assess the impact of environmental factors on cyanobacterial harmful blooms (CyanoHABs) dynamics in a typical shallow lake, Lake Taihu. A sub-pixel approach (algae pixel-growing algorithm) was used with 13 years of MOderate-resolution Imaging Spectroradiometer (MODIS) data to evaluate changes in bloom extension, initiation date, duration, and occurrence frequency before and after a massive bloom event (2007). Results indicated that the conditions after this event changed, with a general delay in bloom initiation and a reduction in bloom duration. The environmental drivers of daily, monthly and inter-annual CyanoHABs dynamics were analyzed by detrended correspondence analysis, principal components analysis and redundancy analysis. This demonstrated that wind speed was the main driver for daily CyanoHABs dynamics, and CODmn, total phosphorus and water temperature were closely related to monthly CyanoHABs dynamics. For the year scale, Tmean and nutrients were the main drivers of CyanoHABs initiation date and duration, and meteorological factors influenced CyanoHABs frequency for the whole lake. Regular monitoring of CyanoHABs by remote sensing has become a key element in the continued assessment of bloom conditions in Lake Taihu, and nutrient reduction policies contribute to decrease CyanoHABs occurrence.