There is increasing recognition that the wide use of nanoparticles, such as Cu (CuNPs) and ZnO nanoparticles (ZnONPs), may pose risks to the environment. Currently there is insufficient insight in the contribution of metal-based nanoparticles and their dissolved ions to the overall toxicity and accumulation. To fill in this gap, we combined the fate assessment of CuNPs and ZnONPs in aquatic test media with the assessment of toxicity and accumulation of ions and particles present in the suspensions. It was found that at the LC50 level of Daphnia magna exposed to the nanoparticle suspensions, the relative contributions of ions released from CuNPs and ZnONPs to toxicity were around 26% and 31%, respectively, indicating that particles rather than the dissolved ions were the major source of toxicity. It was additionally found that at the low exposure concentrations of CuNPs and ZnONPs (below 0.05 and 0.5 mg/L, respectively) the dissolved ions were predominantly accumulated, whereas at the high exposure concentrations (above 0.1 mg/L and 1 mg/L, respectively), particles rather than the released ions played a dominant role in the accumulation process. Our results thus suggest that consideration on the contribution of dissolved ions to nanoparticle toxicity needs to be interpreted with care.