Contaminants may enter surface water through distinct discharges (point sources) or from diffuse (nonpoint) sources such as runoff or contaminated groundwater. While some of the processes that contaminate surface water are obvious since they can be seen, those involving the subsurface generally cannot be directly observed.

Depending on its physical, chemical and biological properties, a contaminant may move within an aquifer in the same ways that groundwater moves.   Some contaminants, however, do not follow groundwater flow.  It is possible to predict, to some degree, the transport within an aquifer of those substances that move along with groundwater flow.  For instance, both water and many contaminants flow from recharge areas to discharge areas.  Soils that are porous and permeable tend to transmit water and certain types of contaminants with relative ease to an aquifer below.

Just as groundwater often moves slowly, so do contaminants in groundwater.  Because of this slow movement and because of non-turbulent flow, contaminants usually remain concentrated in the form of a plume that often flows along the same path as the groundwater.  The size and speed of the plume depend on the amount and type of contaminant, its solubility and density, and the velocity of the surrounding groundwater.

In addition, there is growing concern about the contamination of groundwater through macropores.  These are root systems, animal burrows and other systems of holes and cracks that supply pathways for contaminants.

In areas surrounding pumping wells, the potential for contamination increases because contaminated water in the zone of contribution is drawn into the aquifer and subsequently into the well.  Some drinking water wells maintain an adequate water yield through induced infiltration, whereby water from a nearby stream, lake or river contributes to the well uptake.  Contaminants present in the surface water can degrade the water quality of the aquifer.

Under certain conditions, pumping can cause the groundwater (and associated contaminants) from another aquifer to enter the one being pumped.  This phenomenon is called inter-aquifer leakage.  This may occur when contamination from a shallow aquifer migrates to a deeper aquifer or vice-versa.  Thus, proper well construction along with the accurate location and protection of the areas affected by well pumping are important to the maintenance of groundwater quality.

Usually, the greater the distance between a source of contamination and a groundwater source, the more likely that natural processes will reduce the impacts of contamination.  Processes such as oxidation, biological decay (also called bio-remediation, which sometimes renders contaminants less toxic), chemical reactions and adsorption (binding of materials to soil particles) may take place in the soil layers of the unsaturated zone and reduce the concentration of a contaminant before it reaches groundwater (U.S. EPA, 1990a).  Even contaminants that reach groundwater directly, without passing through the unsaturated zone, can become less concentrated through dilution (mixing) with the groundwater.  Because of the laminar flow usually associated with groundwater, however, contaminants often undergo little dilution.