Soil acidification is the buildup of hydrogen cations, which reduces the soil pH. Chemically, this happens when a proton donor gets added to the soil. The donor can be an acid, such as nitric acid, sulfuric acid, or carbonic acid. It can also be a compound such as aluminium sulfate, which reacts in the soil to release protons. Acidification also occurs when base cations such as calcium, magnesium, potassium and sodium are leached from the soil.

Soil acidification naturally occurs as lichens and algae begin to break down rock surfaces. Acids continue with this dissolution as soil develops. With time and weathering, soils become more acidic in natural ecosystems. The acidic soil can have negative effects on microbial organisms and plant health. Soil acidification rates can vary, and increase with certain factors such as acid rain, agriculture, and pollution. This effect can be prevented through methods such as surface liming, fertilizer reduction, and irrigation.

Rainfall is naturally acidic due to carbonic acid forming from carbon dioxide in the atmosphere. This compound causes rainfall pH to be around 5.0–5.5. When rainfall has a lower pH than natural levels, it can cause rapid acidification of soil. Sulfur dioxide and nitrogen oxides are precursors of stronger acids that can lead to acid rain production when they react with water in the atmosphere. These gases may be present in the atmosphere due to natural sources such as lightning and volcanic eruptions, or from anthropogenic emissions. Basic cations like calcium are leached from the soil as acidic rainfall flows, which allows aluminum and proton levels to increase.

Nitric and sulfuric acids in acid rain and snow can have different effects on the acidification of forest soils, particularly seasonally in regions where a snow pack may accumulate during the winter. Snow tends to contain more nitric acid than sulfuric acid, and as a result, a pulse of nitric acid-rich snow meltwater may leach through high elevation forest soils during a short time in the spring. This volume of water may comprise as much as 50% of the annual precipitation. The nitric acid flush of meltwater may cause a sharp, short term, decrease in the drainage water pH entering groundwater and surface waters. The decrease in pH can solubilize Al³⁺ that is toxic to fish, especially newly-hatched fry with immature gill systems through which they pass large volumes of water to obtain O₂ for respiration. As the snow meltwater flush passes, water temperatures rise, and lakes and streams produce more dissolved organic matter; the Al concentration in drainage water decreases and is bound to organic acids, making it less toxic to fish. In rain, the ratio of nitric-to-sulfuric acids decreases to approximately 1:2. The higher sulfuric acid content of rain also may not release as much Al³⁺ from soils as does nitric acid, in part due to the retention (adsorption) of SO₄^2- by soils. This process releases OH⁻ into soil solution and buffers the pH decrease caused by the added H⁺ from both acids. The forest floor organic soil horizons that are high in organic matter also buffer pH, and decrease the load of H+ that subsequently leaches through underlying mineral horizons.

Plant roots acidify soil by releasing protons and organic acids so as to chemically weather soil minerals. Decaying remains of dead plants on soil may also form organic acids which contribute to soil acidification. Acidification from leaf litter on the O-horizon is more pronounced under coniferous trees such as pine, spruce and fir, which return fewer base cations to the soil, rather than under deciduous trees; however, soil pH differences attributed to vegetation often preexisted that vegetation, and help select for species which tolerate them. Calcium accumulation in existing biomass also strongly affects soil pH - a factor which can vary from species to species.

Certain parent materials also contribute to soil acidification. Granites and their allied igneous rocks are called "acidic" because they have a lot of free quartz, which produces silicic acid on weathering. Also, they have relatively low amounts of calcium and magnesium. Some sedimentary rocks such as shale and coal are rich in sulfides, which, when hydrated and oxidized, produce sulfuric acid which is much stronger than silicic acid. Many coal soils are too acidic to support vigorous plant growth, and coal gives off strong precursors to acid rain when it is burned. Marine clays are also sulfide-rich in many cases, and such clays become very acidic if they are drained to an oxidizing state.

Soil amendments such as chemical fertilizers can cause soil acidification. Sulfur based fertilizers can be highly acidifying, examples include elemental sulfur and iron sulfate while others like potassium sulfate have no significant effect on soil pH. While most nitrogen fertilizers have an acidifying effect, ammonium-based nitrogen fertilizers are more acidifying than other nitrogen sources. Ammonia-based nitrogen fertilizers include ammonium sulfate, diammonium phosphate, monoammonium phosphate, and ammonium nitrate. Organic nitrogen sources, such as urea and compost, are less acidifying. Nitrate sources which have little or no ammonium, such as calcium nitrate, magnesium nitrate, potassium nitrate, and sodium nitrate, are not acidifying.

Acidification may also occur from nitrogen emissions into the air, as the nitrogen may end up deposited into the soil. Animal livestock is responsible for nearly 65 percent of man-made ammonia emissions.