Intertidal flats are important shallow-water habitats and buffers against coastal erosion. Strong, short-lasting meteorological events, such as storms and rainfall, are the main mechanisms of transporting (in)organic materials and sediments. Two in-situ mooring systems were installed simultaneously in the tidal channel and mudflat of Jeungdo, Korea, to understand the dynamic behaviors of suspended sediment and chlorophyll-a (chl-a) under the episodic events. During fair-weather periods with a distinct tidal cycle, the sediment in the mudflat was resuspended during the flood and then advected to the tidal channel during the ebb. The maximum suspended sediment concentration (SSC) and chl-a under storm event were approximately 9 and 2 times higher than those under fair-weather periods, respectively. Under rainfall event, the maxima were approximately 7 and 1.2 times higher than fair-weather, suggesting that sediment and microphytobenthos were highest resuspended by the meteorological events. In addition, a time lag (∼ 1.5 h) between SSC and chl-a occurred in the tidal channel during ebb tide with a rainfall event. During the post-rainfall periods, the SSC and chl-a increased, showing a positive relationship with the bed shear stress, suggesting that the rainfall event could reduce sediment stabilization.