We studied the influence of lotic and lentic stretches on zooseston flux in the karstic barrage Plitvice Lakes (Croatia). Threesampling stretches were selected: 1) a channel with low inclination; 2) water flow through a deep lake (retention), and 3) a channelwith cascades and sharp inclination. At all sampling points of the three stretches, zooseston reached maximum abundance inSeptember (up to 147.39 ind/m3). Rotifers dominated in both zooseston abundance (58 to 80%) and diversity (66 taxa), followedby crustaceans (23 taxa), predominantly Cladocera and Copepoda. Kruskal-Wallis test suggest statistically significant differencesbetween the lentic and both lotic stretches in the biomass net flux of euplanktonic organisms. The net flux of benthicorganism biomass and changes in the biodiversity index were significantly different between the lentic stretch and lotic stretchwith high inclination. Lotic stretches had a greater influence on the increase of abundance and biomass of benthic and semiplanktonicorganisms than on the decrease of euplanktonic organisms. Principal Components Analysis of the species environmentrelationship explained 66% of the variance by the two first axes, where axis 1 accounted for 39% and axis 2 accounted for27% of the variance. Oligochaets, insect larvae, nematodes and total zooseston were associated with component 1, showing thattheir 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, Polyarthraspp., 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 physiographicalfeatures of the stretches, as well as food resources from the lakes.