Spatial and temporal distributions of zooplankton were measured in an oligotrophic pumped storage-type hydroelectric reservoir which was composed of two reservoirs exchanging water daily, with water going up at night and going down during the day. Repetitive diel disturbance of the water column can be a unique feature of this reservoir system. Chl-a concentration was highest in the early winter season. Phytoplankton density was lower in summer monsoon due to high flushing rate on rainy days. The zooplankton density was higher in the smaller upper reservoir possibly due to lower fish density in the upper reservoir. In the seasonal variation a time gap was observed between the phytoplankton bloom and the zooplankton bloom (particularly a rotifer, Keratella cochlearis). It is likely to that Keratella production is partially supported by heterotrophic food sources than phytoplankton. The dominance of a mixotrophic dinoflagellate (Peridinium bipes f. ocultatum) might have complicated the trophic relationship between phytoplankton and zooplankton. Our results provide some ecological information of zooplankton community in a highly disturbed alpine reservoir ecosystem relying on mostly allochthonous organic matter.