Evidence indicates, however, that excessive reliance on monoculture farming and agroindustrial inputs, such as capital-intensive technology, pesticides, andchemical fertilizers, has negatively impacted the environment and rural society. Most agriculturalists had assumed that the agroecosystem/natural ecosystem dichotomy need not lead to undesirable consequences, yet, unfortunately, a number of "ecological diseases" have been associated with the intensification of food production. They may be grouped into two categories: diseases of the ecotope, which include erosion, loss of soil fertility, depletion of nutrient reserves, salinization and alkalinization, pollution of water systems, loss of fertile croplands to urban development, and diseases of the biocoenosis, which include loss of crop, wild plant, and animal genetic resources, elimination of natural enemies, pest resurgence and genetic resistance to pesticides, chemical contamination, and destruction of natural control mechanisms.

Chemical fertilizerscan also become air pollutants, and have recently been implicated in the destruction of the ozone layer and in global warming. Their excessive use has also been linked to the acidification/salinization of soils and to a higher incidence of insect pests and diseases through mediation of negative nutritional changes in crop plants . Use of fertilizers can alter the biology of rivers and lakes. Applied in either liquid or granular form, fertilizer can supply crops with readily available and uniform amounts of several essential plant nutrients. Fertilizers, on the other hand, have been praised as being highly associated with the temporary increase in food production observed in many countries. National average rates of nitrate applied to most arable lands fluctuate between 120-550 kg N/ha. But the bountiful harvests created at least in part through the use of chemical fertilizers, have associated, and often hidden, costs. A primary reason why chemical fertilizers pollute the environment is due to wasteful application and the fact that crops use them inefficiently. The fertilizer that is not recovered by the crop ends up in the environment, mostly in surface water or in ground water. Nitrate contamination of aquifers is widespread and in dangerously high levels in many rural regions of the world. Such nitrate levels are hazardous to human health and studies have linked nitrate uptake to methaemoglobinemia in children and to gastric, bladder and oesophageal cancers in adults.

Pesticides can kill useful insects as well as those that destroy crops. The loss of yields due to pests in many crops. It is well known that cultivated plants grown in genetically homogenous monocultures do not possess the necessary ecological defense mechanisms to tolerate the impact of outbreaking pest populations. Modern agriculturists have selected crops for high yields and high palatability, making them more susceptible to pests by sacrificing natural resistance for productivity. On the other hand, modern agricultural practices negatively affect pest natural enemies, which in turn do not find the necessary environmental resources and opportunities in monocultures to effectively and biologically suppress pests.

Use of chemicals on fields creates run-off, excess runs off into rivers and lakes causing pollution. Fertilizer nutrients that enter surface waters (rivers, lakes, bays, etc.) can promote eutrophication, characterized initially by a population explosion of photosynthetic algae. Algal blooms turn the water bright green, prevent light from penetrating beneath surface layers, and therefore killing plants living on the bottom. Such dead vegetation serve as food for other aquatic microorganisms which soon deplete water of its oxygen, inhibiting the decomposition of organic residues, which accumulate on the bottom. Eventually, such nutrient enrichment of freshwater ecosystems leads to the destruction of all animal life in the water systems.

Per John Jeavons of growbionintensive.org, it kills or malnourishes the fungi and bacteria that hold the soil together, resulting in loss of topsoil, so the increase in yield is only temporary, and, like a heroin addiction, demands ever-greater inputs to sustain output, and eventually destroys the productive capacity of the land.