No known natural processes generate trifluoroacetic acid.  In the environment, trifluoroacetic acid may be formed by photooxidation of the commonly used refrigerant 1,1,1,2-tetrafluoroethane (R-134a). Moreover, it is formed as an atmospheric degradation product of almost all fourth-generation synthetic refrigerants, also called hydrofluoroolefins (HFO), such as 2,3,3,3-tetrafluoropropene. 
Trifluoroacetic acid degrades very slowly in the environment.  Median concentrations of a few micrograms per liter have been found in beer and tea.  Sea water contains about 200 ng of TFA per liter.  No biodegradation mechanism for the compound is known in water, although biotransformation apparently decarboxylates the acid to fluoroform.
Trifluoroacetic acid is mildly phytotoxic.