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Heavy metal lead (Pb) is a primary pollutant that pollutes aquatic environments and can be enriched in aquatic animals. Here, the effects of waterborne Pb on grass carp (Ctenopharyngodon idella) within 96 h of exposure were detected, and the association between microbiota alterations in the intestines and water was analysed. Results revealed that the intestinal barrier was damaged, including the intestinal morphology change, the structure‐related genes (villin‐1 and Claudin‐7) expression down‐regulation, the antioxidant (GST and GSH‐Px) and immune‐related genes (TNF‐α and IL‐8) expression up‐regulation. The MiSeq sequencing data revealed a decrease in diversity and an increase in microbiota richness in the intestines and water after Pb exposure. Linear discriminant analysis (LDA) results revealed an increase in the dominant bacteria (P_proteobacteria and C_Gammaproteobacteria) in the water, which enriched bacteria in the intestines. Canonical correlation analysis (CCA) found that there were correlations between intestinal microbiota and water microbiota, intestinal structure morphology and immune factors. Based on these results, we speculated that the effects of Pb on the grass carp intestinal barrier may be related to changes in the intestinal structure of grass carp and the water microbial community. These findings improve our understanding of the effects of heavy metals on the fish–microbe relationships after polluting aquatic habitats. [ABSTRACT FROM AUTHOR]