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The use of chemicals in a moderate amount isnt harmful, but, when we use it in excess it results in affecting the environment drastically.
Process like leaching etc, degrade the soil and it might reach the underground water level thus causing water pollution.
The soil also loses its natural fertility as the soil is being enriched by chemicals.
The use of chemicals like pesticides,  insecticides etc. help to protect the crops from insects, but it also results in more pest-resistance insects which become potentially more harmful.