Nanotechnology has broadened its horizon by incorporating nanoproducts in agriculture, as it is the primary source of income in developing nations. These nanoparticles (NPs) are incorporated with conventional fertilizers, fungicides, biocides, pesticides, etc., increasing their bioavailability in soil, sediments, and trophic levels. Various kinds of NPs are used in agriculture, for example, inorganic (Cu, Zn, CuO, ZnO, Fe3O4, etc.) and organic. This chapter summarizes, the application of copper-based NPs in agroecosystems. After exposure to the biological system, NPs fate depends on exposure, dissolution, transportation, chemical composition, and interaction with other plants. Their fate can alter depending on the properties of the respective ecosystem they are entering. NPs might aggravate toxic effects on non-targeted plants. Thousands and tons of NPs released into the environment yearly, yet, their interaction with biological systems is needed more systematic and methodical research.