This study is aiming to improve the understanding of hydrodynamic circulation in large shallow lakes. The Lake Taihu, the third largest lake in east China, is picked up as the study area for three reasons. The basin of Lake Taihu is considered as the most populated and developed area as a backyard of Shanghai. Lake Taihu is a typical shallow lake with average water depth of 1.9m. The lake is suffering from severe ecological problems during the past 20 years caused by the growing industrial, agricultural and urban waste water. Literature review showed that in the previous researches over the Lake Taihu, more emphasize was put on resulting concentration of contaminants and nutrients in the water while the hydrodynamic circulation are less quantitatively focused. In this study, hydrodynamic circulation indices are applied to quantify hydrodynamic circulation in Lake Taihu. This study has been carried out through various empirical modeling, schematized modeling and complete 3d modeling approach. To quantify the water circulation and water exchange in the lake, hydrodynamic circulation indices, such as water age and residence time, are introduced. To evaluate the hydrodynamic circulation indices, a simple schematized model is first set up and analyzed to demonstrate the functions and characteristics of different circulation indices. Model input data such as water level, inflow/outflow discharge (mass balance), and land reclamation are analyzed. Since the wind is generally regarded as the driving force for shallow lakes, wind input data is emphasized and corrected for land-measured data. The contribution of different conditions, including various wind conditions, to the water exchange between the lake water and water body discharged from the canals, is evaluated. Then a three-dimensional hydrodynamic model for Lake Taihu is set up and has been calibrated with water level data of year 2008. The three-dimensional hydrodynamic model is used to demonstrate the hydrodynamic circulation pattern in Lake Taihu. Sensitivity tests on the input data and physical parameters shows that the discharge is the most important factor if the wind is not driven force under normal wind conditions. Innovative engineering measurements and design scenarios are proposed to enhance the water circulation, which will potentially promote the water quality in certain subzones of the lake. These design scenarios, including recovery of land reclamation, global dredging, local barrier, local trenches and submerged reef, are investigated. It is found that, although the anthropogenic changes on bed don’t provide global improvement in circulation indices, local improvement is generally observed in subzones of the lake. Furthermore, wave effects are assessed via an empirical nomogram model, a schematized model and a wave model for the Lake Taihu. Results and analysis show that wave effects are not significant for Lake Taihu under normal wind conditions. This study applies hydrodynamic circulation indices to quantify the circulation in Lake Taihu, thus to improve the understanding the hydrodynamic circulation pattern in the lake. This approach could be extended to the hydrodynamic studies in similar large, shallow lakes. The modeling tools are essential for further environmental, biological and ecological study. They are also quantitative tools to assess anthropogenic effects on large shallow lakes for researchers, managers and stakeholders.