Multi-walled carbon nanotubes (MWCNTs), widely used in several industrial fields, are not readily degradable thus, persist in environmental matrices, serving as a source of environmental toxicity to organisms. However, the effects of environmental weathering on nanomaterial toxicity remain unclear. Herein, we prepared aged-MWCNTs (a-CNTs) by incubating commercial pristine-MWCNTs (p-CNTs) for two years and compared their changes in physicochemical properties and toxic effects on zebrafish. The characterization of a-CNTs by transmission electron microscopy, X-ray photoelectron spectra, Raman spectroscopy, and Fourier-transform infrared spectroscopy showed an increased surface area, pore size, structural defects, and surface oxidation than those of p-CNTs. Zebrafish were exposed to 100 mg/L p-CNT and a-CNT for four days. Subsequently, the mRNA expression of antioxidant enzymes, including cat, gst, and sod, in a-CNT group increased by 1.5- to 1.7-fold, consistent with increased expression of genes associated with inflammation (interleukin-8) and apoptosis (p53) compared to control. The higher toxicity of a-CNTs to zebrafish than p-CNT might be due to the increased oxidative potential by altered physicochemical properties. These findings provide new insights into the risk assessment and environmental management of MWCNTs in the aquatic environment. However, further testing at environmentally relevant doses, different exposure durations, and diverse weathering parameters is warranted.