Lake Manyas is an important area for bird conservation, due to its location along the world wide migratory waterbird route. Heavy cyanobacterial blooms occur in this highly turbid and shallow lake during summer and early autumn months, and excessive fish kills were observed after the blooms. The purpose of the present study was to characterize the zooplankton fauna of the pelagic food web to its relationship with selected water quality variables, and to evaluate its contribution to the food chain namely as abundance and diversity in a hypereutrophic shallow lake. Zooplankton and water samples were collected bimonthly at five stations from the open water of the lake between July 2010 and February 2012. During the study period a total of 48 taxa were recorded (3 taxa for Copepoda, 6 taxa for Cladocera, and 39 taxa for Rotifera). Rotifera was the most abundant group of the zooplankton community, comprising 81.2% of all samples, followed by Copepods 10.3% and Cladocerans 8.5%. Zooplankton community of the lake was dominated by eurytopic euplanktonic species Keratella cochlearis (21.8%). According to the Q(B/T) index, Lake Manyas showed a eutrophic character (Q(B/T)=2.3). The outcome of the statistical analysis showed that zooplankton fauna and its abundance were influenced mainly by water temperature, suspended particulate matter, and Secchi disk depth (transparency), respectively. The dense turbidity of Lake Manyas may be responsible for the elimination of sensitive organisms (larger sized cladocerans and copepods) over time, and also allow the dominancy of rotifers. Moreover cyanobacterial blooms affected crustaceans negatively, through poor food quality and harmful toxins. Temperature had a positive effect on rotifers as a result of population growth rates and available food. Consequently, the main factors that altered the composition and abundance of zooplankton in Lake Manyas were determined to be physical variables and favorable food availability.