In order to determine the influence of lentic habitats and macrophyte stands on the plankton development and seston flux, an investigation of zooplankton was carried out in the karst Jankovac flow-through system (Papuk Nature Park, Croatia). The system was characterized by low abundance (1–116 ind.L−1) and high diversity of identified zooplankton. Eighty-six taxa were recorded, comprising 57 rotifers, 15 cladocerans, 8 copepods and 6 members of other groups of organisms. The spatial oscillations of environmental parameters and biocoenosis assemblage revealed statistically significant differences between lotic and lentic habitats, as well as between vegetated and non-vegetated stations. These differences mainly respond to higher concentration of food resources and zooplankton/zooseston abundance and biomass in lentic, especially vegetated, habitats. This is also proved by results of principal component analysis (PCA), which suggested that the main drivers of development of the planktonic community were the food resources and the avoidance of flow velocity. Accordingly, shoreline areas with submerged macrophyte stands of Hippuris vulgaris L. were the most productive parts, represented by highest zooplankton abundance, biomass and biodiversity. Flow velocity significantly affected crustaceans assemblage, so that higher abundances of the larger cladocerans and copepods were achieved in vegetated stations with low flow velocity, while rotifers showed to be rheotolerance organisms. On the other hand, the longitudinal discontinuum of the stream channel by two man-made reservoirs could offer new habitats to enrich seston with organic particles and bioseston. The results of our study pronounce the need for further monitoring of this hydrosystem, especially considering biodiversity and microhabitats conservation.