The calibrated Andong Reservoir hydro-dynamic module (PART I) of the 2-dimensional hydrodynamic and water quality model, CE-QUAL-W2 [v3.2], was applied to examine the dynamics of total phosphorus, and chlorophyll $alpha$ concentration within Andong Reservoir. The modeling effort was supported with the data collected in the field for a five year period. In general, the model achieved a good accuracy throughout the calibration period for both chlorophyll ${alpha}$ and total phosphorus concentration. The greatest deviation in algal concentration occurred on $10^{th}$ October, starting at the layer just beneath the surface layer and extending up to the depth of 35 m. This deviation is principally attributed to the effect of temperature on the algal growth rate. Also, on the same date, the model over-predicts hypolimnion and epilimnion total phosphorus concentration but under-predicts the high concentrated plume in the metalimnion. The large amount of upwelling of finer suspended solid particles, and re-suspension of the sediments laden with phosphorus, are thought to have caused high concentration in the epilimnion and hypolimnion, respectively. Nevertheless, the model well reproduced the seasonal dynamics of both chlorophyll a and total phosphorus concentration. Also, the model tracked the interflow of high phosphorus concentration plume brought by the turbid discharge during the Asian summer monsoon season. Two different hypothetical discharge scenarios (discharge from epilimnetic, and hypolimnetic layers) were analyzed to understand the response of total phosphorus interflow plume on the basis of differential discharge gate location. The simulated results showed that the hypolimnetic discharge gate operation ($103{sim}113;m$) was the most effective reservoir structural control method in quickly discharging the total phosphorus plume (decrease of in-reservoir concentration by 219% than present level).