To understand the variation of total phosphorus and the factors influencing total phosphorus in large, shallow, eutrophic lakes, two years of monthly investigation and one month of daily investigation was carried out in Lake Taihu, China. High temporal variations of total phosphorus in surface water were observed, ranging from 42 microg/L to 250 microg/L during the two years of monitoring at the center of the lake, and 134 microg/L to 737 microg/L during the one month of monitoring in Meiliang Bay during the algal bloom season. High variation in phytoplankton biomass during the bloom season significantly affected total-phosphorus concentration in lake water. The accumulated total phosphorus in algae may be caused by the release from sediment during the blooms. Intensive sediment resuspension caused by wind-induced waves also had significant effects on total phosphorus. Therefore, care should be taken when using total phosphorus or ratios of total nitrogen to total phosphorus for trophic state evaluation in large, shallow and eutrophic lakes.