Because of the strength of the carbon–fluorine bond, organofluorines endure in the environment. Perfluorinated compounds (PFCs) have attracted particular attention as persistent global contaminants.  These compounds can enter the environment from their direct uses in waterproofing treatments and firefighting foams or indirectly from leaks from fluoropolymer production plants (where they are intermediates). Because of the acid group, PFCs are water-soluble in low concentrations.  While there are other PFAAs, the lion's share of environmental research has been done on the two most well-known: perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA).  The U.S. Environmental Protection Agency classifies these materials as "emerging contaminants" based on the growing but still incomplete understanding of their environmental impact.
Trace quantities of PFCs have been detected worldwide, in organisms from polar bears in the Arctic to the global human population.  Both PFOS and PFOA have been detected in breast milk and the blood of newborns.  A 2013 review showed widely varying amounts of PFOS and PFOA in different soils and groundwater, with no clear pattern of one chemical dominating. PFC concentrations were generally higher in areas with more human population or industrial activity, and areas with more PFOS generally also had more PFOA.  the two chemicals have been found at different concentrations in different populations; for example, one study showed more PFOS than PFOA in Germans, while another study showed the reverse for Americans. PFCs may be starting to decrease in the biosphere: one study indicated that PFOS levels in wildlife in Minnesota were decreasing, presumably because 3M discontinued its production.
In the body, PFCs bind to proteins such as serum albumin. Their tissue distribution in humans is unknown, but studies in rats suggest it is present mostly in the liver, kidney, and blood. They are not metabolized by the body but are excreted by the kidneys. Dwell time in the body varies greatly by species.  Rodents have half-lives of days, while in humans they remain for years. Many animals show sex differences in the ability to rid the body of PFAAs, but without a clear pattern. Gender differences of half lives vary by animal species.
The potential health impact of PFCs is unclear. Unlike chlorinated hydrocarbons, PFCs are not lipophilic (stored in fat), nor genotoxic (damaging genes). Both PFOA and PFOS in high doses cause cancer and the death of newborns in rodents. Studies on humans have not been able to prove an impact at current exposures. Bottlenose dolphins have some of the highest PFOS concentrations of any wildlife studied; one study suggests an impact on their immune systems.
The biochemical causes of toxicity are also unclear and may differ by molecule, health effect, and even animal. PPAR-alpha is a protein that interacts with PFAAs and is commonly implicated in contaminant-caused rodent cancers.
Less fluorinated chemicals (i.e. not perfluorinated compounds) can also be detected in the environment. Because biological systems do not metabolize fluorinated molecules easily, fluorinated pharmaceuticals like antibiotics and antidepressants can be found in treated city sewage and wastewater. Fluorine-containing agrichemicals are measurable in farmland runoff and nearby rivers.