Chemical fertilizers are detrimental to the environment. Particularly nitrogen (N), a major polluting factor of water, responsible for the extinction of bio diversity in the aquatic environment. Excessive phospate (P) is also responsible at large.

Water is carrying N and P elements which remain active nutrients. Those nutrients feed all plants in the aquatic environment which proliferate and in turn saturate their own environment leaving particularly limited amount of oxygen for other living organisms. Overtime these other living organisms disappear (for instance fish, shells). See eutrophisation (enrichment of water).

Chemical fertilizers are also detrimental to the soil as over usage of chemical will destroy micro organisms, killing the soil overtime which become sterile. The erosion of the soil in agricultural environment is mostly due to the usage of chemicals. Chemical fertilizers also have huge deficiencies in many micro-nutrients, particularly trace elements.