Cyanobacteria Aphanizomenon population is widely distributed in the world, and well known as harmful algae by producing toxins and off-flavor materials, thus belonging to one of the taxa that became more interested in the field of limnoecology. In this study, the frequency, intensity, and duration of Aphanizomenon occurrence were increased with the abnormal drawdown of water level in the winter in Boryeong Reservoir, and the spatial and temporal characteristics of them are compared with each other in the perspective of hydrometeorology (1998 to 2017) and limnology (2010 to 2017). In Korea, Aphanizomenon flourished mainly in high temperature, and the appearance in the low temperature was rare in total five times. The harmful cyanobacteria Aphanizomenon was observed in the low temperature (December to February) in Boryeong Reservoir from 2014, and then reached a maximum value of 2,160 cells mL-1 in January 2017. In addition, the period exceeding 1,000 cells mL-1 at this time was more than 3 months. This was simultaneously associated with abnormal water level fluctuation in the low temperature (<10℃). The large drawdown of water level in the winter season has the potential to promote or amplify the germination and development of harmful algae. Also, subsequent water quality and ecological impacts (e.g., algal toxins and off-flavor substances) need to be considered carefully.