Abstract Short‐term copper exposure episodes can occur in aquaculture systems due to copper sulfate application or accidental increases in waterborne copper concentrations. However, the temporal patterns of tissue‐specific physiological responses and gut microbiota alterations during acute copper exposure remain insufficiently characterized. Here, we examined copper‐associated responses in gibel carp under a semi‐static exposure with complete daily renewal (control: 0.01 ± 0.00 mg/L; Cu1: 1.25 ± 0.01 mg/L; Cu2: 2.58 ± 0.02 mg/L) at 48 h and 96 h. At 48 h, copper was mainly elevated in the gills and was accompanied by branchial injury and early changes in intestinal microbial composition. At 96 h, hepatic copper increased and coincided with oxidative stress, lipid metabolic disturbance, apoptosis‐related responses, reduced microbial richness, and enrichment of opportunistic bacterial taxa. Spearman correlations indicated associations among tissue copper burden, hepatic injury indicators, and microbiota composition. Overall, this study demonstrates that acute copper exposure induces coordinated physiological and microbiota responses in gibel carp, revealing distinct response patterns among tissues and the gut microbiota over the exposure period.