In order to determine the optimal water intake point, the distribution of blue-Green algae and water quality factors in relation to the depth of the Mulgum and Maeri stations located downstream of the Nakdong River were investigated from Jun. 2015 to Sep. 2016. When the current surface water intake system was converted to the deep water intake system, Chl-a concentration and blue-Green algae were reduced by 64.1% and 80.5%, respectively. Microcystin-LR was reduced by 50% to 100%, while geosmin and 2-MIB of the odorant substances were reduced by 42.9% and 11.8%, respectively. The water quality factors such as pH, water temperature, TOC and COD were gradually decreased by 30% in deep water. Therefore, if we used the deep water intake system selectively in the summer season when blue-Green algae masses occur, the concentration of the influx of blue-green algae and its by-products can be expected to decrease, leading to reduced operation costs in tap water production and improved of raw water quality.