Some of the synthetic compounds used to manufacture fertilizers also have negative environmental effects when allowed to run off into water sources. For instance, ammonia nitrogen and nitrate are main pollutants in rivers and lakes, which leads to eutrophication and ground water pollution. Because it is water-soluble and can remain in groundwater for decades, the addition of more nitrogen over the years has an accumulative effect.

Groundwater contamination has been linked to gastric cancer, birth malformations, hypertension, testicular cancer and stomach cancer. One of the negative effects of fertilizers is called methemoglobinemia or Blue Baby Syndrome. The risk most often occurs when infants are given formula reconstituted with nitrate contaminated water. The condition causes a decrease in oxygen in the blood and results in a blue-grey skin color, causes lethargy and can lead to coma or death.

Well managed organic farming systems with better nutrient retentive abilities (with application of organic fertilizer, for instance), greatly reduce the risk of groundwater pollution. In some areas where pollution is a real problem, conversion to organic agriculture is highly encouraged as a restorative measure.

Fertilizer is one of the three major drivers of biodiversity loss this century. Biodiversity loss may lead to changes in ecosystem functioning, with concordant threats to the stability and resilience of agricultural systems.

A paper published in the journal Nature shows that the world’s grasslands are being destabilized by fertilization. Scientists have identified excessive fertilisation of soils is resulting in a loss of plant diversity. Researches also show that amount of inorganic fertilizer use per hectare of arable land is significantly related to increasing biodiversity risk, especially related plants and soils ecosystems.

The number of studies on organic farming and biodiversity increased significantly since the past one decade. Numerous studies indicate that organic farming produces more biodiversity than other farming systems. The impact of organic agriculture on natural resources favours interactions within the agro-ecosystem that are vital for both agricultural production and nature conservation. Ecological services derived include soil forming and conditioning, soil stabilization, waste recycling, carbon sequestration, nutrients cycling, predation, pollination and habitats.

By opting for organic products such as organic fertilizer, the consumer through his/her purchasing power promotes a less polluting agricultural system. The hidden future environmental costs of agriculture (chemical based) to the environment can thus, be reduced.