The therapeutic use of DEL immersion is intended to manage various diseases caused by parasites in the gills of farmed crucian fish, such as Sinergasilus spp and Ichthyophthirius multifiliis. Although, limited knowledge on the impact of prolonged exposure to DEL on the commensal microbiome and gill injury of early-stage crucian carp. Herein, in this study, we aimed to (a) investigate the detrimental impacts of chronic DEL exposure on the histological, mucosal barrier, inflammation, and apoptosis of the gill of crucian carp and (b) elucidate the differential expression profiling of proteins and the fluctuation of commensal microorganisms in the gill mucosa through the application of proteomic and 16S rDNA sequencing techniques.