The volcano contains three striking summit crater lakes of varying colors. Tiwu Ata Mbupu (Lake of Old People) is usually blue and is the westernmost of the three lakes. The other two lakes, Tiwu Nuwa Muri Koo Fai (Lake of Young Men and Maidens) and Tiwu Ata Polo (Bewitched or Enchanted Lake) are separated by a shared crater wall and are typically green or red respectively. The lake colors vary on a periodic basis. Subaqueous fumaroles are the probable cause of active upwelling that occurs at the two eastern lakes.
Kelimutu is also of interest to geologists because the three lakes are different colors yet are at the crest of the same volcano. According to the local officer at Kelimutu National Park, the colour changes as a result of chemical reactions resulting from the minerals contained in the lake perhaps triggered by volcano gas activity.