The cultivation of apple trees needs to use phytosanitary products, which are used in an irrational way by certain farmers. The harmful effects of pesticides result mainly from their persistence in the environment. Several studies have been carried out to estimate the pesticide residues and assess their effects on soil microorganisms and aquatic organisms. The results of these studies have revealed a harmful effect on these bioindicators. Therefore, a disruption in their growth and reproduction, an increase in their mortality, and a decrease in their fertility have been proven. In addition, a considerable reduction in the number and diversity of soil microorganisms and aquatic organisms has been claimed. Other indicators, such as fish, have shown an accumulation of pesticide residues in their tissues, which can create a danger to human health. Wherefore, it is important to take into account both toxicological and ecotoxicological effects in the environment.