This paper examines spatial and temporal variations of zooplankton abundance and community structure from December 2014 to November 2015 after the opening of the water channel. So, this is the first zooplankton study after the opening of the water channel from the Istanbul Strait to the Golden Horn Estuary. It is thought that this study will be an important database for future studies in the region. A total of 40 species were identified during in this study. Nine species (Daphnia curvirostris, Daphnia hyalina, Bosmina (Eubosmina) coregoni, Cyclops abyssorum, Mnemiopsis leidyi, Pleurobrachia pileus, Beroe ovata, and Aurelia aurita) are first recorded in the Golden Horn and one of these (Bosmina (Eubosmina) coregoni) is also first records for the Turkish coasts. Furthermore, it has been observed that marine zooplankton abundance and diversity have increased in the estuary after the opening of the water channel.