To evaluate substance toxicity, it is critical to maintain specific concentrations of test substances throughout the exposure period. During the last decade, the need to improve methods for nanoparticle (NP) suspension preparations has gained attention because many published results on NPs toxicity have been inconsistent. Here, we compared the toxicity of citrate-coated silver nanoparticles (AgNPs) suspended by two different methods (fractionated vs. colloidal) in freshwater organisms (daphnia and medaka). Analytical methods (ICP-OES, DLS and UV absorbance) were employed to characterize behavior of AgNPs in suspension. Results showed that fractionated (stirred and settled) solution was less toxic to daphnia (13.8 µg/L) than colloidal solution (6.1 µg/L), suggesting that method of preparation was a critical factor that affected toxicity. However, differences in toxicity caused by suspension methods were not observed in medaka. Results indicate that the method used to prepare suspensions of NPs can affect toxicity, and that differences can exist among test organisms.