River eutrophication and CyanoHABs are severe problems that are often ignored because of high current speed and strong self‐purification. In this paper, Liangxi River, Taihu Basin, was selected as the research area. Combined with field investigation, a 2D water environment mathematical model was developed to simulate the chl‐a distribution in Liangxi River. An indicator (Transverse Distribution Center, TDC) and its normalized form (NTDC) to quantitatively represent material transverse distribution in rivers is proposed and coupled in the model. The calculation showed that TDC and NTDC had the property of random fluctuation, seasonal consistency, and water transfer dependence. The multiple regression equation with normalized data indicated that the maximum offset, average variation rate, and average reverting rate of Liangxi River chl‐a NTDC were most affected by the chl‐a dry matter flux ratio between tributaries and the mainstream, followed by flow and chl‐a concentration ratio. From the perspective of river morphology, for different river width change modes and river bending directions, when water flows into and out of these river sections, the chl‐a transverse distribution is subject to different specific effects. In addition, the position of nutrients and dissolved oxygen significantly affected the position of chl‐a growth when the N/P ratio was not very high. Conversely, a high N/P ratio may contribute to decrease of the chl‐a concentration. Proliferation with abundant nutrients may cause the settlement of chl‐a resulting in a decrease of chl‐a in the water column.