Polyculture chemicals into the environment such as eutrophication of fresh water or the presence of excess atmospheric nitrogen are greatly reduced in polycultures. Other negative impacts of modern agriculture are similarly reduced. Excessive tillage occurs in most modern agricultural practices, but removes essential microbes and nutrients from the soil that are conserved in polycultures, especially permacultures. Agricultural machinery not only uses fossil fuels and creates waste, but is more costly to farmers. Because polyculture relies on natural systems of crop maintenance these costs can be eliminated as well. Modern agriculture is also dependent on a very limited number of plant species.
Baltic Sea hypoxia lack of oxygen (anoxia) kills bottom-living organisms and creates dead zones. The rapid increase in hypoxia in coastal areas around the world is due to the excessive inputs of plant nutrients, such as nitrogen and phosphorus by human activities. The sources of these nutrients include agriculture, sewage, and atmospheric deposition of nitrogen containing compounds from the burning of fossil fuels. The nutrients stimulate the growth of algae causing problems with eutrophication. The algae sink to the bottom and use the oxygen when they decompose. If mixing of the bottom waters is slow, such that oxygen stocks are not renewed, hypoxia