The differences in the toxicity of cobalt oxide nanoparticles (Co-NPs) of two different sizes were evaluated in the contexts of the activities of bacterial bioluminescence, xyl-lux gene, enzyme function and biosynthesis of β-galactosidase, bacterial gene mutation, algal growth, and plant seed germination and root/shoot growth. Each size of Co-NP exhibited a different level of toxicity (sensitivity) in each biological activity. No revertant mutagenic ratio (greater than 2.0) of Salmonella typhimurium TA 98 was observed under the test conditions in the case of gene-mutation experiments. Overall, the inhibitory effects on all five bacterial bioassays were greater than those on algal growth, seed germination, and root growth. However, in all cases, the small Co-NPs showed statistically greater (total average about two times) toxicity than the large Co-NPs, except in shoot growth, which showed no observable inhibition. These findings demonstrate that particle size may be an important physical factor determining the fate of Co-NPs in the environment. Moreover, combinations of results based on various biological activities and physicochemical properties, rather than only a single activity and property, would better facilitate accurate assessment of NPs’ toxicity in ecosystems.