This study examined the seasonal dynamics of the bacteria, Synechococcus spp. and their nanoflagellate grazers in the Danshui River estuary in northern Taiwan and compared the variations in microbes (bacteria, Synechococcus spp. and nanoflagellate) dynamics under different (clear vs. stormy) weather conditions. Temporal variations in chlorophyll a concentrations, bacterial production, bacteria and Synechococcus spp. abundance were related to temperature, with higher values during the warmer seasons. Spatial variations in Synechococcus spp. were related to chlorophyll a concentrations and in bacterial production and abundance related to chlorophyll a concentrations when temperature is above 20°C (April, August, and October). Spatial variations in nanoflagellates were related to oscillations in bacterial abundance or production during non-rainy periods. We conclude that heavy freshwater input to the estuary carries a large quantity of riverine bacteria which might disrupt the relationship between bacterial and nanoflagellate abundance during rainfall events.