© 2023 John Wiley & Sons, Ltd.The mechanisms of various metal nanoparticles (NPs) are still a matter of debate in aquatic toxicology. In order to close this gap, the number of studies on this subject is increasing. The aims of this study are to explore the interactions of PdCu@f-MWCNT NPs with zebrafish and get to know if it has an ecotoxicological risk. In this study, we synthesized, characterized PdCu@f-MWCNT NPs, and investigated its ecotoxicological effects. The chemical and morphological structures of PdCu@f-MWCNT nanomaterials were elucidated with advanced analysis techniques such as scanning electron microscope (SEM), X-ray spectrophotometer (EDX), transmission electron microscope (TEM), and X-ray diffraction (XRD) analyses. The ecotoxicological risks were investigated by conducting biochemical analyses and malformation defects in zebrafish. The results were obtained using multiple marker applications including oxidative stress parameters, proinflammatory cytokine expressions, DNA damage, and apoptosis markers. The obtained findings showed embryonic development, survival rate, and incidence of malformation increasing in parallel with the dose increase in zebrafish exposed to PdCu@f-MWCNT NPs at 10–1000 μg/L levels. Despite the observed decreases in antioxidant enzyme activities, GSH level, AChE activity, and NRF-2 level, inductions in malondialdehyde (MDA) level, IL-6, TNF-α, NF-kB, DNA damage, and apoptosis levels were observed with increasing dose. Considering these findings, it has been determined that there are toxic effects in zebrafish at all levels above the concentration that we examine as a safe dose (10 μg/L). The effects of all studied concentrations of this NP above the safe dosage, especially on oxidative stress, malformation, and immune system, were found to be quite significant. The more widespread use of nanotechnology in the future will mean more contact of aquatic organisms with NPs. As a result, it is clearly seen that these organisms, which form the important link of the food chain, and the aquatic environment are living at risk conditions.