Frequent algal blooms at major river systems in Korea have been serious social and environmental problems. Especially, the appearance of cyanobacteria with toxic materials is a threat to secure a safe drinking water. In order to model the behaviour of cyanobacteria cell number, an exclusive causality analysis using prewhitening technique was introduced to delineate effective parameters to predict the cell numbers of cyanobacteria in Seungchon Weir and Juksan Weir along Youngsan river system. Both input and output transfer function models were obtained to explain temporal variation of cyanobacteria cell number. A threshold behaviour of water temperature was implemented into the model development to consider winter characteristic of cyanobacteria. The implementation of water temperature threshold into the model structure improves the predictability in simulation. Even though the input output transfer model cannot completely explained all blooms of cyanobacteria, the simple structure of model provide a feasibility in application which can be important in practical aspect.