Silver nanoparticles (AgNPs) inevitably discharge into aquatic environments due to their abundant use in antibacterial products. It was reported that in laboratory conditions, AgNPs display dose-dependent toxicity to aquatic organisms, such as bacteria, algae, macrophytes, snails and fishes. However, AgNPs could behave differently in natural complex environments. In the present study, a series of microcosms were established to investigate the distribution and toxicity of AgNPs at approximately 500 mg L1 in aquatic systems. As a comparison, the distribution and toxicity of the same concentration of AgNO3 were also determined. The results showed that the surface layer of sediment was the main sink of Ag element for both AgNPs and AgNO3. Both aquatic plant (Hydrilla verticillata) and animals (Gambusia affinis and Radix spp) significantly accumulated Ag. With short-term treatment, phytoplankton biomass was affected by AgNO3 but not by AgNPs. Chlorophyll content of H. verticillata increased with both AgNPs and AgNO3 short-term exposure. However, the biomass of phytoplankton, aquatic plant and animals was not significantly different between control and samples treated with AgNPs or AgNO3 for 90 d. The communities, diversity and richness of microbes were not significantly affected by AgNPs and AgNO3; in contrast, the nitrification rate and its related microbe (Nitrospira) abundance significantly decreased. AgNPs and AgNO3 may affect the nitrogen cycle and affect the environment and, since they might be also transferred to food web, they represent a risk for health.