Triclosan (TCS) is a common disinfectant in consumer products, raising concerns about its effects on aquatic life. This study assessed the accumulation and impact of TCS on zebrafish (Danio rerio) by examining histological, biochemical, and NMR-based metabolomic changes in gill and intestinal tissue after 30 d of exposure to environmental concentrations (30, 50, and 70 µg/L). Both tissues showed TCS accumulation, which resulted in histopathological damage. The activity of catalase, lactate dehydrogenase, and acetylcholinesterase increased, while superoxide dismutase and glutathione S-transferase declined. Conversely, the content of malondialdehyde rose, but soluble protein decreased. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis displayed a varied spectrum of protein profiles, demonstrating alterations in the cytoskeletal proteins. Fourier-transform infrared spectroscopy indicated concentration-dependent alterations in the cytoskeletal protein secondary structures. Gene expression studies revealed alterations in the mRNA expression of genes associated with oxidative stress (sod-Cu/Zn, cat and mgst3b), metabolism (ldha), neural activity (ache), and cytoskeletal dynamics (actn4, myl9a, tpma, tuba1b and desmb). Nuclear magnetic resonance spectroscopy revealed significant changes in metabolic pathway profiles, validated by amino acid analysis. These results suggest that TCS can disrupt aquatic ecosystems by inducing oxidative stress, affecting cytoskeletal dynamics, and modifying metabolic processes.