In this study, the impact of nanoparticles on the chemical behavior of metals in a tropical coastal environment was evaluated in a microcosm assay. The microcosms were assembled to reproduce the original environmental conditions, to evaluate the effects of two different nanoparticles. The aquariums were filled with water and sediment from Cunha River (Rio de Janeiro – Brazil) - which is highly contaminated by metals and organic compounds - and nanoparticles of hydroxyapatite (500 nm) and poly lactic-co-glycolic acid (PLGA) nanoparticles doped with Holmium-166 (200 nm), both radiolabeled with 99mTc. The quantification of trace metals (Cu, Zn, Mn, Fe, Cr and Pb) was performed in the water samples. The concentration data obtained for Fe, Cr and Pb were lower than ICP-OES Detection Limits (Fe: DL < 0.0343 mg.L−1, Cr: DL < 0.0036 mg.L−1 and Pb: DL < 0.0291 mg.L−1), while the results for Cu, Zn and Mn demonstrated that the presence of hydroxyapatite and PLGA nanoparticles had no influence on the behavior of dissolved metals, probably because of the high organic loads of the system, which may have overwhelmed or masked the interaction of nanomaterials with metals, once the natural organic matter could interact with the nanoparticles, favoring their aggregation and sedimentation and thus reducing their bioavailability and reactivity. Geochemical fractionation presented a relevant association of metals with the organic phase. In terms of environmental impact assessment of nanomaterials, it was concluded through 99mTc labelling that both nanomaterials (about 30% to 50%) remained in solution during the 49 h of the experiment.