Based on the COHERENS (a Coupled Hydrodynamical Ecological model for Regional Shelf seas), a three-dimensional baroclinic model for the summer of East China Sea (ECS) was established with the sigma-coordinate in the vertical direction and spherical coordinate in the horizontal direction. The circulation patterns of the Kuroshio Current, the Taiwan Warm Current (TWC), the Tsushima Current and the Yangtze Diluted Water (YDW) were successfully simulated with this model. The calculated results are fairly consistent with previous observations and studies. Based on this baroclinic current field, the Lagranian particles tracking was simulated to estimate the possible origins of the red tides frequently occurring in the Yangtze River estuary and its adjacent sea areas. If there are “seeds” (cysts) of the red tide algae at the seabed of the Taiwan Strait, the offshore of Fujian and Zhejiang Provinces and the northeast Taiwan Island, those are extremely possible sources of the red tides in the Yangtze River estuary and its adjacent sea areas. Field data are needed to confirm it. Numerical simulation to estimate the source of the red tides is a new application of the Lagrangian transport in the marine ecology. Based on the COHERENS (a Coupled Hydrodynamical Ecological model for Regional Shelf seas), a three-dimensional baroclinic model for the summer of East China Sea (ECS) was established with the sigma-coordinate in the vertical direction and spherical coordinates in the horizontal direction The circulation of the Kuroshio Current, the Taiwan Warm Current (TWC), the Tsushima Current and the Yangtze Diluted Water (YDW) were successfully simulated with this model. The calculated results are fairly consistent with previous observations and studies. Based on this baroclinic current field, the Lagranian particles tracking was simulated to estimate the possible origins of the red tides frequently occurring in the Yangtze River estuary and its adjacent sea areas. If there are “seeds” (cysts) of the red tide algae at the seabed of the Taiwan Strait, the offshore of Fujian and Zhejiang Provinces and the northeast Taiwan Island, those are extremely possible sources of the red tides in t he Yangtze River estuary and its adjacent sea areas. Field data are needed to confirm it. Numerical simulation to estimate the source of the red tides is a new application of the Lagrangian transport in the marine ecology.