Despite progress in evaluation of risk assessment, knowledge gaps largely exist understanding the toxicity of nanoplastics in aquatic systems considering nanoplastics surface properties, environmental media characteristics and species ecological traits. In this study, amidine -functionalized polystyrene nanoparticles (PS-NPLs) of 20, 40, 60 and 100 nm are considered using Geneva lake water and mineral water to investigate the behavior and effects in neonate organisms of the plankton Daphnia magna and the benthos Gammarus fossarum. Key parameters including zeta-potential, z-average diameter, conductivity, polydispersity index, pH, EC50 were investigated. The results showed that the toxicity of PS-NPLs exhibited a dose-response relationship, size-and exposure condition-dependent trend. The smaller size PS-NPLs (20 and 40 nm) induced higher adverse effects than PS-NPLs of 60 and 100 nm in both water conditions and crustacean species. Moreover, PS-NPLs were found more toxic in the mineral water compared to lake water. Principal component analysis evidenced that the surface charge and aggregation behavior are the most influential toxicity of PS-NPLs factor for D. magna and Gammarus fossarum, respectively. These results highlight the relationship between PS-NPLs intrinsic properties, their transformation behavior, water properties and species-specificity in the evaluation of PS-NPLs biological effects on crustacean neonates in natural aquatic environments.