Pesticides are essential compounds in modern agriculture used as plant protection products that minimize pests, weeds, and diseases while maintaining long-term crop productivity. Once introduced, they can persist and circulate through biogeochemical processes, often with far-reaching ecological consequences. However, the widespread use of pesticides has raised contamination concerns, posing a significant risk to ecosystems, biodiversity, and food safety due to their persistence. This chapter provides a review of the scientific literature, offering insights into recent trends and future challenges associated with pesticide use in modern agriculture, with a focus on individual elements (water, soil, and air) and organisms (plants, microorganisms, and humans). Furthermore, the article provides examples of herbicide behavior in soil, as well as the sorption, degradation, and leaching mechanisms associated with microbiota-mediated degradation. According to these findings, it is possible to suggest that uncontrolled pesticide use may harm non-target organisms, as described in scientific literature. However, more research into the environmental consequences of these compounds is required to complete the knowledge gap on this topic.