Chemical fertilizers create an imbalance of nutrients in the environment. They can also cause the soil's pH level to rise.
Using chemical fertilizers for an extended period can cause the balance of the ecosystems to change. More pests may gather in the area. Also, chemical fertilizers require repeated application as they tend to run off after some time. The repeated treatments could cause an accumulation of chemicals. Many nutrients that are in the fertilizer are already found in the soil. Therefore, using the fertilizer causes there to be an abundance of nutrients in the soil as well, which may pose a risk to sensitive plants.