We studied the influence of lotic and lentic stretches on zooseston flux in the karstic barrage Plitvice Lakes (Croatia). Three sampling stretches were selected: 1) a channel with low inclination; 2) water flow through a deep lake (retention), and 3) a channel with cascades and sharp inclination. At all sampling points of the three stretches, zooseston reached maximum abundance in September (up to 147.39 ind/m3). Rotifers dominated in both zooseston abundance (58 to 80%) and diversity (66 taxa), followed by crustaceans (23 taxa), predominantly Cladocera and Copepoda. Kruskal-Wallis test suggest statistically significant differences between the lentic and both lotic stretches in the biomass net flux of euplanktonic organisms. The net flux of benthic organism biomass and changes in the biodiversity index were significantly different between the lentic stretch and lotic stretch with high inclination. Lotic stretches had a greater influence on the increase of abundance and biomass of benthic and semiplanktonic organisms than on the decrease of euplanktonic organisms. Principal Components Analysis of the species environment relationship explained 66% of the variance by the two first axes, where axis 1 accounted for 39% and axis 2 accounted for 27% of the variance. Oligochaets, insect larvae, nematodes and total zooseston were associated with component 1, showing that their biomass was negatively correlated with discharge and dissolved oxygen concentration and positively correlated with temperature. Other taxa showed a similar correlation with component 1. Biomass of Cladocera, Copepoda, T. birostris, Polyarthra spp., K. cochlearis and rotifers was associated with component 2, and positively correlated with food resources such as chl-a, POM and DOM. The inference is that zooseston flux through Plitvice Lakes is a function of the hydrological and physiographical features of the stretches, as well as food resources from the lakes.