Ciprofloxacin (CIP), one of the most frequently detected antibiotics in water systems, has become an aquatic contaminant because of improper disposal and excretion by humans and animals. It is still unknown how trace amounts of CIP affect the aquatic microbial community diversity and function. We therefore investigated the effects of CIP on the structure and function of freshwater microbial communities via 16S/18S rRNA gene sequencing and metatranscriptomic analyses. CIP treatment (7 μg/L) did not significantly alter the physical and chemical condition of the water body as well as the composition of the main species in the community, but slightly increased the relative abundance of cyanobacteria and decreased the relative abundance of eukaryotes. Metatranscriptomic results showed that bacteria enhanced their phosphorus transport and photosynthesis after CIP exposure. The replication, transcription, translation and cell proliferation were all suppressed in eukaryotes, while the bacteria were not affected in any of these aspects. This interesting phenomenon was the exact opposite to both the antibacterial property of CIP and its safety for eukaryotes. We hypothesize that reciprocal and antagonistic interactions in the microcosm both contribute to this result: cyanobacteria may enhance their tolerance to CIP through benefiting from cross-feeding and some secreted substances that withstand bacterial CIP stress would also affect eukaryotic growth. The present study thus indicates that a detailed assessment of the aquatic ecotoxicity of CIP is essential, as the effects of CIP are much more complicated in microbial communities than in monocultures. CIP will continue to be an environmental contaminant due to its wide usage and production and more attention should be given to the negative effects of antibiotics as well as other bioactive pollutants on aquatic environments. Keywords: Ciprofloxacin, Cyanobacteria, Meta-transcriptomic analysis, High-throughput sequencing, Freshwater microbiome