Copper oxide nanoparticles (CuO-NPs) are widely used for their catalytic properties, conductive capacity, and innovations in the fields of superconductors, alloys, and solar energy sensors. To better understand the impact of water chemistry on the stability of CuO nanoparticles, a series of measurements were carried out on nanoparticles suspended in pure water, natural water, and water enriched with natural organic matter fulvic acid (FA). ICP-MS characterization in single-particle mode (SP-ICP-MS) was performed to determine the stability or transformation of nanoparticles in contrasting water conditions. We first observed that particle sedimentation was very fast in pure Milli-Q water. The addition of FA favored the dissolution of CuO-NPs with an increase in the dissolved copper concentration, for both Milli-Q water and natural water. The presence of FA also reduced the size of CuO-NPs (i.e., less aggregation) measured in natural water. By comparing signals of single particles, FA decreased nanoparticle numbers as well, confirming the increase in dissolution of CuO-NPs over time. The transformation products of CuO-NPs are important in the ecological context since the uptake and toxicity of parent nanoparticles differ from those of the chemical species in solution. Further considerations are needed on the fate of released NPs to better assess their exposure pathways to aquatic organisms and potential environmental risks.