Over a three-year period (2007–2009), in-situ measurements were taken and water-quality samples were collected from 111 lakes and wetlands located in the Yukon Flats, Alaska, during a U.S. Fish and Wildlife Service wetlands inventory. The U.S. Geological Survey performed the chemical analyses on the retrieved water-quality samples. Results from the analyses of water samples for dissolved carbon gases and carbon isotopes, hydrogen and oxygen stable isotopes, dissolved organic carbon, and major cations and anions, along with supporting site data, are presented in this report.