The aim of this study was to determine the relationships in the microbial trophic network underpinning them about communities of plankton ciliates in shallow oxbow lakes of the Vistula River in southern Poland (Jeziorzany 1, Jeziorzany 2, Piekary, Tyniec). The plankton components (phytoplankton, ciliates, zooplankton) were grouped by dietary preference. The studied oxbows differed in physicochemical parameters and in phytoplankton. Cyanobacteria dominated in the total biomass of phytoplankton in the Tyniec oxbow, big green algae (>30 μm) in Piekary and Jeziorzany 1, and euglenoids in Jeziorzany 2 oxbow. The dominance pattern of ciliates and zooplankton were similar in all oxbows. Algivorous ciliates were the main dominant ciliates, and among zooplankton the dominant ones were herbivores that feed on small algae (<30 μm). The oxbows differed significantly in total phytoplankton biomass, cyanobacteria biomass, euglenoid biomass, small green algae (<30 μm) biomass, total biomass of zooplankton, biomass of zooplankton feeding on bacteria + algae, and biomass of zooplankton feeding on big algae (>30 μm). There was no significant differences in ciliate biomass between oxbows. In redundancy analyses, the variability at the trophic groups of plankton was described by explanatory variables in 42.3 %, and positive relationships were found: e.g., between omnivorous zooplankton biomass, the biomass of ciliates feeding on bacteria + algae, and NH4 level; between euglenoid biomass and dinoflagellate biomass; and between cyanobacteria biomass and bacterivorous ciliate biomass. Spearman correlation analysis revealed several relationships between different groups of plankton. In general, phytoplankton group shows more connection among themselves and with different zooplankton groups, e.g., phytoplankton biomass with herbivorous zooplankton biomass (−0.33); and cyanobacteria biomass with dinoflagellate biomass (0.65). Ciliates showed more connections among their trophic groups (e.g., algivorous ciliate biomass with omnivorous ciliate biomass, 0.78) and with zooplankton trophic groups (e.g., biomass of algivorous + bacterivorous ciliates with biomass of predator zooplankton, −0.36). Simple correlations analysis revealed the trophic food web network connectivity among plankton organisms, indicating the flow of organic matter from phytoplankton to zooplankton and from ciliates to zooplankton. Our study sheds light on the trophic relations among plankton ciliates, which are neglected in research but often form a large percentage of zooplankton biomass. In the studied oxbows, ciliate forms 6.7 % of total zooplankton biomass in Jeziorzany 1 and up to 44.5 % of it in the Piekary oxbow.