Fertilizers partially restore plant nutrients lost by erosion, crop harvesting, and leaching. Farmers can use either organic fertilizer from plant and animal materials or commercial inorganic fertilizer produced from various minerals. Three basic types of organic fertilizer are animal manure, green manure, and compost. Animal manure includes the waste matter of cattle, horses, poultry, and other farm animals. It improves soil structure, adds organic nitrogen, and stimulates beneficial soil bacteria and fungi.

Despite its effectiveness, the use of animal manure in the United States has decreased. There are three reasons for this: the replacement of most mixed animal-raising and crop-farming operations with separate operations for growing crops and raising animals, the high costs of transporting animal manure from feedlots near urban areas to distant rural crop-growing areas, and the replacement of horses and other draft animals that added manure to the soil with tractors and other motorized farm machinery.

Green manure is fresh or growing green vegetation plowed into the soil to increase the organic matter and humus (degraded organic matter) available to the next crop. Compost is a sweet-smelling, dark-brown, humuslike material that is rich in organic matter and soil nutrients. It is produced when microorganisms in soil (mostly fungi and aerobic bacteria) break down organic matter such as leaves, food wastes, paper, and wood in the presence of oxygen. Compost is a rich natural fertilizer and soil conditioner that aerates soil, improves its ability to retain water and nutrients, helps prevent erosion, and prevents nutrients from being wasted by being dumped in landfills. Compost is produced by piling up alternating layers of nitrogen-rich wastes (such as grass clippings, weeds, animal manure, and vegetable kitchen scraps), carbon-rich plant wastes (dead leaves, hay, straw, sawdust), and topsoil. Compost provides a home for microorganisms that help decompose plant and manure layers and reduces the amount of plant wastes taken to landfills and incinerators.

Another form of organic fertilizer is the spores of mushrooms, puffballs, and truffles. Rapidly growing and spreading mycorrhizae fungi in the spores attach to plant roots and help them take in moisture and nutrients from the soil. Unlike typical fertilizers that must be applied every few weeks, one application of mushroom fungi lasts all year and costs just pennies per plant. The fungi also produce a bigger root system, which makes plants more disease resistant.

Corn, tobacco, and cotton can deplete the topsoil of nutrients, especially nitrogen, if planted on the same land several years in a row. One way to reduce such losses is crop rotation. Farmers plant areas or strips with nutrient-depleting crops one year. In the next year they plant the same areas with legumes, whose root nodules add nitrogen to the soil. In addition to helping restore soil nutrients, this method reduces erosion by keeping the soil covered with vegetation and helps reduce crop losses to insects by presenting them with a changing target.

Today, many farmers rely on commercial inorganic fertilizers containing nitrogen (as ammonium ions, nitrate ions, or urea), phosphorus (as phosphate ions), and potassium (as potassium ions). Inorganic commercial fertilizers are easily transported, stored, and applied. Worldwide, their use increased about tenfold between 1950 and 1989 but declined by 12% between 1990 and 1999. Today, the additional food they help produce feeds one of every three people in the world, without them, world food output, would drop an estimated 40%.

Commercial inorganic fertilizers have some disadvantages, however. These include (1) not adding humus to the soil, (2) reducing the soil’s content of organic matter and thus its ability to hold water (unless animal manure and green manure are also added to the soil), (3) lowering the oxygen content of soil and keeping fertilizer from being taken up as efficiently, (4) typically supplying only two or three of the twenty or so nutrients needed by plants, and (5) releasing nitrous oxide, a greenhouse gas that can enhance global warming. The widespread use of commercial inorganic fertilizers, especially on sloped land near streams and lakes, also causes water pollution as nitrate and phosphate fertilizer nutrients are washed into nearby bodies of water. The resulting plant nutrient enrichment causes algae blooms that use up oxygen dissolved in the water, thereby killing fish.

肥料可以恢复部分因侵蚀，作物收获和淋溶而损失的植物养分。农民可以使用植物和动物材料中的有机肥料，也可以使用各种矿物质生产的商业无机肥料。有机肥的三种基本类型是动物粪肥，绿肥和堆肥。包括牛，马，家禽和其他农场动物的排泄物的动物粪便能够改善土壤结构，增加有机氮的含量，刺激有益土壤的细菌和真菌的繁殖。 尽管它非常有效，但在美国使用动物粪便作为肥料的情况已经减少。三种原因造成这种情况：将大多数混养动物饲养和作物种植业务分别替换为单独种植作物和饲养动物；将动物粪便从城市附近的饲养场运送到遥远的农作物种植区；以及用拖拉机和其他机动农用机械替代马和其他动物来向土壤添加粪肥。 绿肥是犁入土地的新鲜的或者正在生长的绿色植物，以增加下一作物可利用的有机物和腐殖质（降解的有机物质）的量。堆肥是一种有甜味，深褐色，富含腐殖质的物质，富含有机质和土壤养分。它是由土壤中的微生物（主要是真菌和需氧细菌）在氧气存在下分解有机物质如叶子，食物垃圾，纸张和木材时产生的。堆肥是一种丰富的天然肥料和土壤调理剂，能够增加土壤的通气性，提高其保留水分和养分的能力，可防止侵蚀，并防止养分由于被倾倒在垃圾填埋场中而浪费。堆肥是通过堆积富含氮肥的废物（如草屑，杂草，动物粪便和蔬菜厨余废料），富含碳的植物废料（枯叶，干草，稻草，锯末）和表土而形成的。堆肥为微生物提供了家园，有助于分解植物和粪肥层，并减少垃圾填埋场和焚化炉中的植物废物量。 另一种有机肥形式是蘑菇，马勃菌和松露的孢子。孢子中的菌根真菌附着于植物根部且快速增长，并帮助它们从土壤中吸收水分和养分。与每隔几周就要施用的典型肥料不同，蘑菇真菌一次的施用可以持续一年，每株植物的成本仅为几分钱。真菌还会产生更大的根系，使植物更加抗病。 如果连续几年种植在同一片土地上，玉米，烟草和棉花可能会耗尽其表层营养物质，尤其是氮。有一种方法可以减少这种损失，那就是轮作。第一年农民在这片土地上种植营养消耗作物。在第二年，在同样的地区种植豆科植物，这样可以让其根部结节向土壤中添加氮。除了帮助恢复土壤养分，这种方法还通过保持土壤覆盖植被而减少了侵蚀，并通过不断为害虫提供变化的目标而有助于减少损失。 今天，许多农民都在依靠含氮（如铵离子，硝酸根离子或尿素），磷（如磷酸根离子）和钾（如钾离子）的商业无机肥料。无机商品肥料易于运输，储存和施用。无机商品肥料的使用量在1950年至1989年间在世界范围内增加了十倍左右，但在1990年至1999年间下降了12％。今天，得益于无机肥料而额外增加的粮食数量足以喂养世界上的三分之一的人口，而没有他们，世界粮食产量就会下降40％。 然而，商业无机肥料有一些缺点。包括它（1）不向土壤中添加腐殖质，（2）减少土壤中有机物质的含量，从而降低土壤的持水能力（除非动物粪便和绿肥也加入土壤中），（3）降低氧气（4）通常仅供应植物所需的二十种或三种营养物质中的两种或三种，（5）释放一氧化二氮（一种可加剧全球变暖的温室气体）。由于硝酸盐和磷肥等营养物质被冲入附近水体，商业无机肥料的大量使用还会造成水质污染，特别是在溪流和湖泊附近的斜坡地区。由此产生的植物养分富集引起藻类水华会消耗掉溶解在水中的氧气，从而杀死鱼类。