In this study, results are presented for depth-specific hydraulic and water quality surveys, as well as meteorological observations, at key monitoring sites in the Paldang Reservoir, South Korea. These results were used to determine the water circulation characteristics that represent the main contributors to water quality changes. In the section before the confluence point of the two rivers, a different type of two-layer flow appeared for each. In the North Han River, backwater flowing backward in the upstream direction occurred in the surface layer, and was accompanied by two-layer flow, during the zero-discharge period of the Cheongpyeong Dam. On the other hand, in the South Han River, two-layer flow was observed in the upper layer in the downstream flow, and the thickness of upper and lower layers varied depending on the discharge rate of the Paldang Dam. Strong flow fluctuations were observed near the Paldang Dam (3 km upstream), and these were dependent on its instantaneous discharge rate. In particular, if the instantaneous discharge from the Paldang Dam remained below 400 m3/s for several days, the flow velocity in the lower layer decreased below 2 cm/s or no flow occurred. The comparison between flows during different periods associated with depth-specific water temperature variations showed that the average flow prevailed across all layers in the downstream direction at all monitoring sites during the vertical mixing period. In contrast, spatiotemporal variations in flow, such as two-layer flow and backwater, were observed during the stratification period in the South Han River and the North Han River. This led to increased residence times and vertical stability, thus creating favorable conditions for algal blooms.