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Water quality problems in the Xiaowan Reservoir due to a recently built dam of upper Mekong River have became major ecological and economic concerns. The main goal of this work was thus to describe the present water quality and metazooplankton dynamics and to evaluate the effects of damming on aquatic ecosystem in the super reservoir. The water quality including conductivity, turbidity, Chlorophyll a, dissolved oxygen, total nitrogen, total phosphorus and metazooplankton communities were surveyed along the 30 km away from the dam in the reservoir from 2011 to 2012. Throughout our study, most of the water quality parameters showed clear temporal changes. The total nitrogen and phosphorus showed mean values of 0.9 and 0.04 mg L–1 at different sites. The dominated species of zooplankton showed typical seasonal succession. The most important factor in the determination of zooplankton throughout the year is water temperature and Chlorophyll <em>a</em>. The spatial distribution of water quality parameters and zooplankton communities fluctuated considerably among different sites. However, it is difficult to explain these spatial changes which may relate to the unstable water conditions. Our results showed that the area along the 30 km away from the dam of Xiaowan Reservoir belonged to lake-type environment. More attention should be paid on the aquatic ecosystems of the reservoirs which belong to the gorge area with high mountains and steep valleys.