Most of Korea’s rivers and lakes are subject to physico-chemical disturbances, such as increased water quantity and flow rates, and influx of nitrogen and phosphorus, due to intense rainfall concentrated in the Asian monsoon season. To examine the influence of rainfall on epilithic diatom communities, we measured the diatom distribution and river water quality at 29 sites along the main-stream and tributaries of the Hantangang River, Korea, in the period of 2012–2015. Water quality parameters in the polluted sites had improved following rainfall, but the response of dominant species varied with water quality; the dominant species Nitzschia fonticola decreased in abundance regardless of sampling sites, and the abundance of Achnanthidium minutissimum in the clean sites and Nitzschia palea in the polluted sites increased after rainfall, respectively. The community dynamic index (CDI) showed that the most obvious shift of epilithic diatom community occurred in the mid-polluted sites in 2013 with the highest rainfall. This suggest that the effect of rainfalls on the epilithic diatom community is dependent on various parameters, such as the magnitude of rainfall, water quality and its biotic compositions of diatom communities, but it also indicates that improving the water quality of rivers is important to promote the resilience of diatom communities to extremes of precipitation. Further investigation is needed to generalize the effects of monsoon rainfall on the epilithic diatom communities, considering rivers with different environmental characteristics.