River ecosystems are among the most affected habitats globally by human activities, such as the release of industrial, agricultural and domestic pollutants to the rivers. However, how affected zooplankton functional groups in rivers are largely unknown. In the present study zooplankton functional and taxonomic structure were investigated seasonally in relation to environmental parameters between 2013 and 2015 in Kocagay Delta located on the South of the Marmara Region. The environmental parameters (e.g. water temperature, conductivity, dissolved oxygen, pH, chlorophylla and nutrients) were measured at four sampling station covering estuarine and riverine area. A total of 44 taxa of zooplankton were identified and mostly dominated by cosmopolite microphagous rotifers reflecting the proper intervals of environmental parameters for their habitat chokes. Among rotifers Microcodides chlaena and Keratella serrulata were the new records for the study site and Turkish rotifer list. The only selective filter feeder was Bosmina longirostris in Kocacay Delta. The zooplankton functional group, microphagous, showed seasonal variations and affected by chlorophyll-a content. We suggested that trait-based approaches would be a useful tool to assess the degree of environmental disturbance and interaction between trophic levels.