We studied the populations of the dominant calanoid copepods Pseudodiaptomus annandalei and Acartia spp. in the mesohaline Danshuei Estuary for two successive springs and summers. We analyzed environmental factors (i.e., temperature, salinity, chlorophyll a, light attenuation coefficient, and suspended particulate matter) and the population densities and structures at the surface and near the estuarine bed. The population of P. annandalei dominated the zooplankton community from surface to bottom, except during a medusa bloom in 2009 and during the post-typhoon period, when Acartia spinicauda dominated. The relationships between environmental factors and densities differed between and within populations of P. annandalei and Acartia spp. We concluded that the primary determinants of the P. annandalei population are predation and the typhoon-related freshwater runoff, which can strongly influence the copepod succession in this part of the estuary.