Purpose The intensive development of nanotechnology raises a question of the potential consequences of the presence of nanoparticles (NPs) in the different components of the environment, including sediments. The aim of this study was to evaluate the toxicity of nanoparticles of ZnO and Ni and their bulk counterparts in bottom sediments (SD1, SD2) with different properties collected from the Vistula River in Poland. Materials and methods Sediment samples with NPs at a concentration of 100 mg kg −1 were incubated for 17 months in the dark or under a photoperiod of 12 h light/12 h dark. The Microtox ® (bacteria, Vibrio fischeri) and OSTRACODTOXKIT F ™ (ostracods, Heterocypris incongruens) tests were used to evaluate toxicity. In addition, the contents of Zn and Ni were determined in extracts (H 2 O and CaCl 2 ) of the bottom sediments. Results and discussion The Zn concentration was much lower in the SD1 sediment with the addition of NPs/bulk particles (30-230 μg kg −1 ) compared to the SD2 sediment (280-1140 μg kg −1 ). The toxicity of ZnO and Ni was determined by the type of bottom sediment and the parameter studied.Both nano-and bulk-ZnO and Ni caused the mortality of H. incongruens at a level of 13.3-53.3 %. The influence of ZnO and Ni on the growth of H. incongruens was observed to be the opposite. ZnO resulted in growth stimulation, while Ni resulted in growth inhibition of H. incongruens. Both ZnO and Ni stimulated V. fisheri luminescence. In most cases, the incubation of ZnO and Ni under the photoperiod increased the toxicity or decreased the stimulation of V. fisheri bioluminescence and H. ingongruens growth compared to the darkincubated sediments. Conclusions The study provides new and important information on the ecotoxicological effects of ZnO and Ni nanoparticles in different sediments and under various environmental conditions that may be useful for the risk assessment of this new group of contaminants.