Outbreaks of blue algae bloom in Taihu Lake have occurred frequently since 2006. Lots of blue algae appeared along the shore of south Taihu Lake from July to November every year, and the highest concentration of algae in water could reach more than 170 million per liter in 2007 and 2008. The worsened water environment, especially during the period of severe eutrophication, not only made the lake basin be faced with the risks of the shortage of high quality drinking water, but also caused the lake reduction of fish species and appearance of smaller, younger or trash fish. South Taihu Lake generally refers to the areas located along the part of the lake in Zhejiang Province, and the water quality data available is very limited compared with those of east or north Taihu Lake for the future concern on the issue. An annual variation of blue algae biomass, NH4+-N and TN levels at Xiaomei, Xintang and Daqian inlet areas of south Taihu Lake was determined at regular intervals so as to find out the water quality conditions and the variation regularity between the blue algae biomass and ammonia nitrogen (NH4+-N) or total nitrogen (TN). The correlation between the blue algae biomass and NH4+-N or TN was analyzed by SPSS 10.0. The results showed that: (1) the blue algae biomass at different inlet areas had two peaks, one in May-June, and the other in September-October each year; (2) water quality was in eutrophic phase due to the high TN level; (3) the correlation coefficient (r) between biomass and NH4+-N level was -0.102 to -0.290, indicating not correlated; (4) the r value between biomass and TN level in 2008—2009 was -0.010 to 0.210, indicating not correlated; and with the r value of -0.430 to -0.474 in 2010, meaning lowly-negative correlated. Attention should be paid to the high nitrate level at different inlet areas of south Taihu Lake. The lake in high concentration of NH4+-N and TN, might provide the conditions for growth and reproduction of blue algae, but in the case of the outbreaks of blue algae bloom, NH4+-N and TN concentrations would decrease rapidly. In south Taihu Lake basin exists the wane and wax regularity between the blue algae biomass and NH4+-N or TN. And the above-mentioned results could provide the necessary data for the analysis of the time and conditions of blue algae bloom in south Taihu Lake and make it possible to provide early warning information for the outbreak of blue algae bloom and water quality deterioration.