The spectral reflectance and water qualities of 27 stations were acquired in the lake Taihu during the months from May to August, 2008 when blue algal bloomed. Based on the fluorescence characteristics analysis of different chlorophyll a concentration, it was obvious that the position and height of fluorescence peak both have a positive correlation with chlorophyll a concentration, and the correlation coefficients between chlorophyll a concentration and position and half width of fluorescence peak are larger than those of the reference baseline and the normalized height of fluorescence. Estimating of chlorophyll a concentration in case 2 water using fluorescence characteristics is obviously better than the empirical algorithm based on blue to green ratio. Moreover, the common algorithm based on near infrared band to red band ratio is essentially consistent with the normalized height method.