Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi in mycoremediation, and plants in phytoremediation), living or dead, is employed for removing environmental pollutants from air, water, soil, fuel gasses, industrial effluents etc., in natural or artificial settings. The natural ability of organisms to adsorb, accumulate, and degrade common and emerging pollutants has attracted the use of biological resources in treatment of contaminated environment. In comparison to conventional physicochemical treatment methods bioremediation may offer advantages as it aims to be sustainable, eco-friendly, cheap, and scalable. This technology is rarely implemented however because it is slow or inefficient.

Most bioremediation is inadvertent, involving native organisms. Research on bioremediation is heavily focused on stimulating the process by inoculation of a polluted site with organisms or supplying nutrients to promote their growth. Environmental remediation is an alternative to bioremediation.

While organic pollutants are susceptible to biodegradation, heavy metals cannot be degraded, but rather oxidized or reduced. Typical bioremediations involves oxidations. Oxidations enhance the water-solubility of organic compounds and their susceptibility to further degradation by further oxidation and hydrolysis. Ultimately biodegradation converts hydrocarbons to carbon dioxide and water. For heavy metals, bioremediation offers few solutions. Metal-containing pollutant can be removed, at least partially, with varying bioremediation techniques. The main challenge to bioremediations is rate: the processes are slow.

Bioremediation techniques can be classified as (i) in situ techniques, which treat polluted sites directly, vs (ii) ex situ techniques which are applied to excavated materials. In both these approaches, additional nutrients, vitamins, minerals, and pH buffers are added to enhance the growth and metabolism of the microorganisms. In some cases, specialized microbial cultures are added (biostimulation). Some examples of bioremediation related technologies are phytoremediation, bioventing, bioattenuation, biosparging, composting (biopiles and windrows), and landfarming. Other remediation techniques include thermal desorption, vitrification, air stripping, bioleaching, rhizofiltration, and soil washing. Biological treatment, bioremediation, is a similar approach used to treat wastes including wastewater, industrial waste and solid waste. The end goal of bioremediation is to remove harmful compounds to improve soil and water quality.

Bioventing is a process that increases the oxygen or air flow into the unsaturated zone of the soil, this in turn increases the rate of natural in situ degradation of the targeted hydrocarbon contaminant. Bioventing, an aerobic bioremediation, is the most common form of oxidative bioremediation process where oxygen is provided as the electron acceptor for oxidation of petroleum, polyaromatic hydrocarbons (PAHs), phenols, and other reduced pollutants. Oxygen is generally the preferred electron acceptor because of the higher energy yield and because oxygen is required for some enzyme systems to initiate the degradation process. Microorganisms can degrade a wide variety of hydrocarbons, including components of gasoline, kerosene, diesel, and jet fuel. Under ideal aerobic conditions, the biodegradation rates of the low- to moderate-weight aliphatic, alicyclic, and aromatic compounds can be very high. As molecular weight of the compound increases, the resistance to biodegradation increases simultaneously. This results in higher contaminated volatile compounds due to their high molecular weight and an increased difficulty to remove from the environment.

Most bioremediation processes involve oxidation-reduction reactions where either an electron acceptor (commonly oxygen) is added to stimulate oxidation of a reduced pollutant (e.g. hydrocarbons) or an electron donor (commonly an organic substrate) is added to reduce oxidized pollutants (nitrate, perchlorate, oxidized metals, chlorinated solvents, explosives and propellants). In both these approaches, additional nutrients, vitamins, minerals, and pH buffers may be added to optimize conditions for the microorganisms. In some cases, specialized microbial cultures are added (bioaugmentation) to further enhance biodegradation.

Approaches for oxygen addition below the water table include recirculating aerated water through the treatment zone, addition of pure oxygen or peroxides, and air sparging. Recirculation systems typically consist of a combination of injection wells or galleries and one or more recovery wells where the extracted groundwater is treated, oxygenated, amended with nutrients and re-injected. However, the amount of oxygen that can be provided by this method is limited by the low solubility of oxygen in water (8 to 10 mg/L for water in equilibrium with air at typical temperatures). Greater amounts of oxygen can be provided by contacting the water with pure oxygen or addition of hydrogen peroxide (H₂O₂) to the water. In some cases, slurries of solid calcium or magnesium peroxide are injected under pressure through soil borings. These solid peroxides react with water releasing H₂O₂ which then decomposes releasing oxygen. Air sparging involves the injection of air under pressure below the water table. The air injection pressure must be great enough to overcome the hydrostatic pressure of the water and resistance to air flow through the soil.

Bioremediation can be carried out by bacteria that are naturally present. In biostimulation, the population of these helpful bacteria can be increased by adding nutrients.