To improve water quality and alleviate eutrophication in Lake Taihu, the third largest freshwater lake in China, a Yangtze River water transfer project was initiated in 2002 to bring water from the Yangtze River to Lake Taihu to dilute and divert pollutants out of the lake. We used a three-dimensional numerical model,Environmental Fluid Dynamics Code, to study the impacts of water transfer on the transport of dissolved substances in the lake by using the concept of water age. In particular, the influences of inflow ributaries and wind forcing on water age were investigated. Model results showed that the effect of water transfer on transport processes in the lake is strongly influenced by hydrodynamic conditions induced by wind and inflow/outflow tributaries. During the simulation year (2005), the water ages in Lake Taihu were highly variable both spatially and temporally, with a mean of approximately 130 days in summer and 230 days in the other seasons. Southeasterly winds—dominant in the summer—could improve the quality of water by reducing the water age in the eastern areas of the lake, which are used as a drinking water source, and in Meiliang Bay, the most polluted bay. In terms of dilution, the most efficient flow rate for transferred water was predicted to be approximately 100m3/s. The spatial distribution of water ages showed that water transfer may preferentially enhance exchanges in some areas of the lake unless nutrient concentrations in the transferred water are reduced to a reasonable level. This study provides useful information for a better understanding of the complex hydrodynamic and mass transport processes in the lake, which is important for developing and implementing effective ecological restoration strategies in the region.