Cu-based fungicides are indispensable in organic food production for the control of plant diseases as well as in integrated food production in order to additionally slow down the process to become resistant to classical organic fungicides. Absorbing Cu in small quantities is proven to be vital for the most organisms, however in higher doses can cause harm. The aim of this thesis is to present the results from various researches on the influence of Cu agents on non-target organisms and some alternative options to mitigate the negative ecological consequences after their long-term use. People who apply Cu fungicides on plants can contribute to the increase of Cu consentration in the soil due to its accumulation. This can cause harmful effects on macro and microfauna and prevent plants from accepting some nutrients. The bioavailability of Cu in the soil is influenced by pH, redox potential, soil texture and quantity of organic matter. Earthworms are more sensitive to Cu than other soil organisms. Cu has a big influence on the activity of soil microorganisms, hence the important processes in the soil are also affected. It also affects differently the entomopathogenic fungi, depending on the type and amount of fungicide and its exposure time. Acquatic organisms are particularly sensitive on increased concentrations of Cu. Although Cu fungicides are difficult to be replaced due to their effectiveness, it is possible to reduce Cu residues in the environment by planting more resistent varieties and using newer formulations of Cu preparations, which are more effective than conventional ones, in accordance to the rules and with the right timing. In order to purify already contaminated soil, phytoremediation or biomineralization can be used, while adsorption processes can be applied for the contaminated water.