This research reviews a copious amount of agricultural studies in which the effects (pros & cons) of pesticide use on the environment are measured. A pesticide is any substance used to kill, repel, or control certain forms of plant or animal life that are considered to be pests. Pesticides affect the environment in numerous ways such as: contamination of soil, water, and vegetation. In addition, pesticides are toxic to many organisms including fish, birds, beneficial insects, and even humans. This paper focuses on the microbial mechanisms of pesticides and connects those biochemical properties (mechanisms) to deregulation of function within organisms, and how that, in turn, affects the environment overall. After reviewing a variety of studies, this paper suggests that pesticide application should be greatly reduced, and, instead, applied in concert with alternative, eco-friendly pesticides such as beneficial insects, biological methods, and transgenic crops to allow the environment to maintain a biogeochemical balance, and microbes to work efficiently.