Although study of the toxicity of metallic nanoparticles in aquatic organisms is increasing, there is still little known about their combined toxicity, especially in a comparative and integrated approach. The objective of this study is to compare the toxicity of copper nanoparticles (CuNP), chromium nanoparticles (CrNP), and their mixtures to crucian carp (Carassius auratus) through a comprehensive approach. A high median lethal concentration of CuNP (390.75 mg/L) and CrNP (551.03 mg/L) was calculated from the acute toxicity, indicative of low toxicity to crucian carp. After exposure for 10 d at sublethal concentrations, several biomarker responses, including the activities of brain acetylcholinesterase (AChE), gill sodium/ potassium-activated ATP (Na⁺/K⁺-ATP), liver superoxide dismutase (SOD), and catalase (CAT) were significantly inhibited by all nanoparticles in most cases, implying the neurotoxicity, osmoregulatory toxicity, and oxidative damage of metallic nanoparticles. Thereafter, the integrated biomarker response version 2 (IBRv2) integrating all biomarker responses was applied to compare the toxicity, and therefore the toxicity order was tentatively proposed as: the mixtures ≈ CuNP＞CrNP, suggesting a synergistic effect in the mixtures. The findings will help to understand the ecological impacts of metallic nanoparticles in an aquatic environment in a more complete and accurate picture.