Many factors control and affect geochemical reactions.

Once in the system, microbial processes continue to slowly alter the structure and chemical reactivity of the organic matter.
An important element of artificial recharge is the introduction of potentially reactive organic matter into an aquifer. Geochemical interactions between this organic matter and aquifer solids inorganic constituents in the subsurface can result in fractionation of the organic matter, thereby altering its composition and the surfaces of aquifer solids. In addition, varying the amount and nature of the organic material in the aquifer may be a significant factor in controlling a number of geochemical, microbial and environmental processes. Due to its reactive nature, a thorough understanding of the biogeochemistry of organic matter in the aquifer is warranted. Here, a description of the factors that control the nature, transport and reactivity of organic matter in the subsurface is presented.

Organic matter in ground water plays important roles in controlling geochemical processes by acting as proton donors/acceptors and as pH buffers, by affecting the transport and degradation of pollutants and by participating in mineral dissolution/precipitation reactions. Dissolved and particulate organic matter also may influence the availability of nutrients and serve as a carbon substrate for microbially mediated reactions. Numerous studies have recognized the importance of natural organic matter in the mobilization of hydrophobic organic species, metals and radionuclides. Many contaminants that scientists view as virtually immobile in aqueous systems can interact with dissolved organic carbon or colloidal organic matter, resulting in migration of hydrophobic chemicals far beyond distances predicted by structure/activity relationships. Although organic matter often is present in low concentrations in subsurface systems, this organic matter can exhibit significant reactivity with contaminants. In addition, these compounds are reactive substances that are potential precursors for the formation of disinfection by-products resulting from water treatment practices.

Organic matter in surface water and ground water is a diverse mixture of organic compounds ranging from macromolecules to low molecular weight compounds, such as simple organic acids and short-chained hydrocarbons. Historically, organic matter in natural waters has been arbitrarily divided into dissolved (DOC) and particulate organic carbon (POC), based on filtration properties. No natural cutoff exists between these two fractions and the distinction is arbitrary, based on the filtration of the sample. The definition of terms, therefore, is operational. Overlapping the dissolved and particulate fractions is the colloidal fraction, which consists of suspended solids that are operationally considered solutes. Colloidal organic matter in natural waters is composed of living and senescent organisms, cellular exudates and partially-to-extensively degraded detrital material, all of which may be associated with mineral phases. Generally, DOC is in greater abundance than POC, accounting for approximately 90 percent of the total organic carbon of most waters.

Microbial degradation of organic matter results in the formation of many of the compounds that comprise DOC, especially non-volatile organic acids that dominate the DOC in most aquatic environments. Many of these organic acids are considered refractory because the rates of subsequent biodegradation are slower than for other fractions or classes of organic matter. Organic matter derived from different source materials has distinctive chemical characteristics associated with those source materials. Organic matter derived from higher plants, for instance, has been found to have relatively large amounts of aromatic carbon, is high in phenolic content and low in nitrogen content. Microbially-derived organic matter (from algae and bacteria), on the other hand, has greater nitrogen content and low aromatic-C and phenolic content. In ground water, there are three main natural sources of organic matter - organic matter deposits such as buried peat, kerogen and coal; soil and sediment organic matter; and organic matter present in waters infiltrating into the subsurface from rivers, lakes and marine systems. The relative contributions of these sources of organic matter varies between different water bodies, but presently there is no way to quantify this variation based on chemical characterization of the organic matter. Once in the system, microbial processes continue to slowly alter the structure and chemical reactivity of the organic matter.

A number of significant, albeit poorly understood, mechanisms can be responsible for the transport or retention of organic molecules in the subsurface. Once in the system, organic compounds, whether they be anthropogenic or naturally derived, can be truly dissolved, associated with immobile particles or associated with mobile particles. Mobile particles include DOC, DOC-iron complexes and colloids. For an organic compound, each state is related to the other states through equilibrium partitioning and air/water exchange. The magnitude of the partitioning coefficients and the abundance of sorbents determine the mechanisms and enhancement of transport for a particular organic compound. Regardless of environment, chemical reactivity and speciation will be controlled by thermodynamics and reaction kinetics.

Application of chromatographic theory to subsurface transport can aid in understanding and quantifying the chemical processes in subsurface systems. Chromatography essentially is the transport of a chemical in a mobile fluid phase through a column packed with a stationary phase. A chemical introduced at the beginning of this column moves at a rate proportional to the average velocity of the fluid and inversely proportional to the strength and nature of sorptive interactions with the stationary phase. These interactions include ionic and complexation interactions, hydrogen bonding, van der Waal's interactions and equilibrium partitioning. In a ground water system, the geologic matrix, representing the stationary phase, generally consists of sand grains coated with organic matter. The mobile phase is the water, which can contain significant quantities of dissolved organic and inorganic chemicals. Organic compounds move through the system as a result of the flow rate of water and the strength and nature of interactions with the stationary phase. The nature and distribution of organic matter in the system is determined, to a large extent, by the interactions between the various phases in the environment.

Although little is known about the nature of the solid-phase coatings, it is important to recognize that the surfaces of the stationary particles have a profound effect on their sorptive properties for organic molecules. Almost all stationary particle surfaces are covered with an organic coating that imparts a negative charge to the surface. A sorptive interaction between organic compounds and stationary phases removes the DOC from solution and changes the surface of the particles. This process is a function of the chemical properties of the DOC, the particle-size distribution and the chemistry of the ground water. Positively charged organic solutes are readily removed from the dissolved phase by cation exchange, which can be a significant sorption mechanism. Organic solutes that may exist as cations in natural waters include amino acids and polypeptides. Hydrophilic neutral (e.g. carbohydrates, alcohols) and low molecular weight anionic organic compounds (e.g. organic acids) are retained the least by aquifer solids. Hydrophobic organic compounds interact strongly with the organic matter associated with the solid-phase. These interactions are controlled, in part, by the nature of the organic coatings, especially with respect to its polarity and aromatic carbon content. Interactions of hydrophobic organic compounds with stationary particles can result in strong binding and slow release rates of these compounds. ND