Periphytic ciliate communities of riverine floodplains have hardly been studied, although they play an important role in aquatic food webs and contribute to the overall ecosystem functioning. In this study we analyzed the taxonomic and functional composition and diversity of these communities across all seasons and hydrological phases. The study was conducted in a floodplain lake, a part of the large natural Danube floodplain, from February 2015 to September 2016. We found that higher temperature and hydrologically stable conditions during the lake isolation phase, when a high amount of suspended food is available, result in the highest ciliate abundances and dominance of relatively large suspension-feeding ciliates, mainly peritrichs, which could serve as good bioindicators for detecting disturbances in river-floodplain ecosystems. During the flow pulse phase, associated with lower temperatures, and during the phase of extreme floods, when the availability of suspended food was largely reduced, small surface-feeding ciliates prevailed in the periphyton. Further, while the total ciliate abundance was the lowest, the highest taxonomic and functional diversity was found, especially during an intermediate level of hydrological connectivity (flow pulse). Our results confirm the importance of different levels of hydrological connectivity for maintaining biodiversity in riverine floodplains and add to a growing awareness of the need to preserve the natural hydrological regimes of large rivers.