We analyzed the effect in physical and chemical environmental factors on relationship between primary producers and herbivores in three station selected along the main channels of the Youngsan River estuary from July 2014 to April 2015. Salinity directly affected by the inputs of freshwater was 20.7 psu at St. A of summer. Chlorophyll-a and nano-sized phytoplankton were high values during this period. The turbidity affected by the tide occurred a high value at St. B and C during the dry season. Hypoxia was not found in this study, but there were difference in density according th the difference in salinity between the surface and bottom layer and the dissolved oxygen was 4 mg/L. This suggests that possibility of stratification and hypoxia. Since zooplankton except for certain species occurred a correlation between Bacillariophyceae and micro-sized phytoplankton, the main feed of zooplankton may be micro-sized Bacillariophyceae. Therefore, it is suggested that phytoplankton is affected by direct environmental factors such as water temperature, turbidity, and salinity, and that zooplankton can be indirectly affected by physical and chemical environmental factors on biological interaction with phytoplankton.