Based on the underwater photosynthetically active radiation (PAR) profile measurement and the concentrations of the optically active substances, the spatial patter and affecting factors of euphotic depth in Lake Taihu are discussed. Phytoplankton primary production (PP_eu) of all the lakes in autumn 2004 is estimated using the vertically generalized production model (VGPM) based on measured surface chlorophyll-a (Chl.a) concentration, euphotic depth, water temperature, PAR at the water surface, photoperiod and water depth. Euphotic depth ranges from 0.37 to 5.27m with a mean value of 1.52±1.06 m. The higher euphotic depth appears in the macrophyte-dominated lake regions such as East Lake Taihu, Xukou Bay and water area between Xishan and Dongshan Islands. In contrast, the lower euphotic depth is found in algal-dominated lake region such as Meiliang Bay and the southwestern open water. The regression analyses show that euphotic depth is mainly controlled by nonpigment particle matter, next to phytoplankton and chromophoric dissolved organic matter (CDOM). Nonpigment particle matter can explain 96.7% variation of euphotic depth. The ranges of Chl.a concentration and estimated PP_eu are 1.21-53.59μg/L, 77.4-2484.9mg/(m²·d), respectively. The estimated daily mean PP_eu distribution coincides closely with that of Chl.a concentration. Higher Chl.a and PP_eu values are recorded in Meiliang Bay and lower values are found in Xukou Bay or southwestern open water. There is a good correlation between VGPM PP_eu and primary production from the empirical model (PP_em)(r² = 0.79, p<0.0001). Daily mean_eu and PP_em of all the lakes are 694.5±492.0, 719.8±315.4mg/(m²·d), respectively. Although the ranges of the two methods differ, the mean values are very close. PP_eu more accurately captures spatial variation by considering the effect of euphotic depth, water temperature, surface PAR and photoperiod on PP.