Besides being a naturally occurring element and an essential micronutrient, copper is used as a pesticide, but at generally higher concentrations. Copper, unlike organic pesticides, does not degrade, but rather enters a complex biogeochemical cycle. In the water column, copper can exist bound to both organic and inorganic species and as free or hydrated copper ions. Water column chemistry affects copper speciation and bioavailability. In all water types (saltwater, brackish water, and freshwater), organic ligands in the water column can sequester the majority of dissolved copper, and therefore, organic ligands play the largest role in copper bioavailability. In freshwater, however, the geochemistry of a particular location, including water column characteristics such as water hardness and pH, is a significant factor that can increase copper bioavailability and toxicity. In most cases, organic ligand concentrations greatly exceed copper ion concentrations in the water column and therefore provide a large buffering capacity. Hence, copper bioavailability can be grossly overestimated if it is based on total dissolved copper (TDCu) concentrations alone. Other factors that influence copper concentrations include location in the water column, season, temperature, depth, and level of dissolved oxygen. For example, concentrations of bioavailable copper may be significantly higher in the bottom waters and sediment pore waters, where organic ligands degrade much faster and dissolved copper is constantly resuspended and recycled into the aquatic system. Aquatic species differ greatly in their sensitivity to copper. Some animals, like mollusks, can tolerate high concentrations of the metal, while others are adversely affected by very low concentrations of copper. Emerging evidence shows that very low, sublethal copper levels can adversely affect the sense of smell and behavior of fish. The developmental stage of the fish at the time of copper exposure is critical to the reversibility of sensory function effects. The fish olfactory system may be the most sensitive structure to copper pollution. The major factors that influence copper-induced toxicity are dissolved organic carbon and water salinity. Dissolved organic carbon reduces copper toxicity by sequestering bioavailable copper and forming organic complexes with it. Salinity, on the other hand, influences copper bioavailability at the biological action site and also affects metal biodistribution and bioaccumulation in the organism. Therefore, the salinity gradient can increase or decrease copper toxicity in different aquatic species. In some killifish, copper may affect different organs at different times, depending on the water salinity. The most studied and best explained copper toxicity mechanisms involve inhibition of key enzymes and disruption of osmoregulation in the gill. Other toxicity mechanisms may involve reactive oxygen species generation and changes of gene transcription in the fish olfactory signaling pathway. More studies are needed to evaluate the potential magnitude of copper remobilization from the sediment that may result from climate change and its effects on surface waters. Moreover, the environmental exposure, fate, and ecotoxicity of emerging metal nanoparticles, including nanocopper, will require additional studies as new forms of copper appear from application of nanotechnology to copper compounds.