We evaluated changes in the phytoplankton community in Korean coastal waters during October 2016 and February 2017. Typhoon Chaba introduced a large amount of freshwater into the coastal areas during autumn 2016, and there was a significant negative relationship between salinity and nutrients in the Nakdong estuarine area, particularly in the northeastern area (Zone III; p < 0.001). The abundance of diatom species, mainly Chaetoceros spp., increased after this nutrient loading, whereas Cryptomonas spp. appeared as opportunists when there was relatively low diatom biomass. During winter, biotic and abiotic factors did not differ among the surface, middle, and lower layers (p > 0.01; ANOVA), implying that water mixing by winter windstorms and low surface temperature (due to the sinking of high-density water) physically accelerated mixing of the whole water column. Diatoms predominated under these conditions. Among diatoms, the centric diatom Eucampia zodiacus remained at high density at the inshore area and its abundance had a negative correlation with water temperature, implying that this species can grow at cold temperatures. On the other hand, the harmful freshwater diatom Stephanodiscus hantzschii mainly appeared in conditions with low salinity and high nutrients, implying that it can persist even in the saltwater conditions of the Nakdong Estuary. Our results indicate that hydro-oceanographic characteristics, such as river discharge after an autumn typhoon and winter water turbulence, have major effects on the composition of phytoplankton communities and can potentially affect the occurrence and characteristics of harmful algal blooms in southern Korean coastal waters.