This work presents results on synthesis of isotopically enriched (99% (65)Cu) copper oxide nanoparticles and its application in ecotoxicological studies. (65)CuO nanoparticles were synthesized as spheres (7 nm) and rods (7 × 40 nm). Significant differences were observed between the reactivity and dissolution of spherical and rod shaped nanoparticles. The extreme sensitivity of the stable isotope tracing technique developed in this study allowed determining Cu uptake at exposure concentrations equivalent to background Cu concentrations in freshwater systems (0.2-30 μg/L). Without a tracer, detection of newly accumulated Cu was impossible, even at exposure concentrations surpassing some of the most contaminated water systems (>1 mg/L).