The fate and toxicity of nanoparticles (NPs) in the aquatic systems mainly depend on the eco-corona formed on NP surface upon entry. This eco-corona could be composed of numerous environmental components but the most common is natural organic matter (NOM). NOM is bulky organic compound with a high-intensity negative charge on its surface that absorbs on NPs and stabilizes them by mainly steric hindrance and electrostatic repulsion between NPs. NOM, being a natural entity, can increase the biocompatibility of NPs with aquatic organisms. The high-intensity negative charge on NOM-NP complex can also reduce their toxicity to the aquatic organisms by declining their bioavailability. The toxicity of NPs has been observed to be more drawn to lower trophic organisms of microbial and invertebrate food chains including the embryos of fish. In recent years, the bioaccumulation and biomagnification of NPs have also been demonstrated as a critical factor in the toxicity assessment of NPs. Here, we summarize the fate and toxicity of NPs in aquatic systems in relation to bare and NOM-modified NPs.