Long and short term investigations have revealed dramatic changes in fish communities after impoundments by reservoirs. However, the process of these changes during impoundment remains poorly studied. In 2005 and 2006, before and during the second stage of impoundment of the Three Gorges Reservoir (TGR), in the upper reaches of the Yangtze, China, we investigated fish catches to assess the impacts of reservoir filling on fish community structure. We conducted sampling at 2 sites, Wanzhou reach, which had been inundated by the first water filling in 2003, and Fuling reach, which still remained a riverine site before this water filling. The results revealed an evident and immediate shift of fish communities from lotic to lentic components. In the Wanzhou reach, during the filling, the abundance percentage of lentic fish increased to 94% compared to 69% before the filling. In the Fuling reach, after the filling, lotic fish declined in abundance from 99% to 85%, while lentic fish increased from less than 1% to 12% in abundance. Based on our investigation and the regulation scheme of the TGR, we predicted that after the completion of the Three Gorges Dam (TGD), there would be typical lacustrine, transitional and riverine zones in TGR, with their corresponding fish assemblages. We suggest that long term monitoring should be conducted to evaluate the future ecological effects, and different strategies implemented in these three zones for conservation purposes.