PFAAs including branched isomers occurred ubiquitously in an entire water cycle. PFAAs contaminated confined aquifers 20–800 m below ground level. Short-chain PFAAs tended to contaminate surface water more than groundwater. The PFAAs patterns in confined aquifers differed from those in other water bodies. Confined aquifers may be a safer source of tap water with the restrictions on PFOS.