A new upwinding finite element numerical models which is two-dimensional and suitable for calculating concentrations of total phosphorus (TP) in shallow lakes considering major controlling factors of a dvection, dispersion, deposition and releasing from bottom, is derived. Moreover it is used in the research on the characteristics and effecting factors of TP distribution in Taihu Lake. Main results are:(1) The model presented is reasonable, valid and cost-effective; (2) Lake current produces certain impact on TP distribution in Taihu Lake. In general. the flow patterns dominated by anticlockwise circulation with a higher speed (velocity) are more beneficial to TP transportation and dispersion process; (3) rhe ability of diluting purification of the open water in Taihu Lake is much stronger than that of Meiliang Bay; (4) Major factors affecting TP concentration are different from region to region in Taihu Lake briefly, in the waterfield to the west of the line of Daojiao Hill-Dalei Hill-Xingtang. the major controlling factors are hydraulic transportation and dispersion, and to the east of the line of Marivshan Island-West Hill-Zheshan Hill it is the releasing from the bottom sediment.