The Tri-Colored Crater Lakes of Kelimutu, Indonesia occupy the summit craters of the Kelimutu Volcano on Flores Island, Indonesia. Although the three lakes are adjacent to one another, each is differently colored, and the colors periodically change, also independently from one another. The color changes are suspected to be attributed to chemical changes in the lake waters from interactions between dissolved minerals and volcanic gas eruptions.
The three lakes are named Tiwi Ata Mbupu (Lake of Old People), Tiwu Nua Muri Kooh Tai (Lake of Young Men and Maidens) and Tiwu Ata Polo (Lake of Evil Spirits, or Enchanted Lake).
Of course, as volcanic lakes, I'd make them reeking, corrosive, poisonous, bubbling up with asphyxiating (or perhaps explosive) gasses, and a lovely place to visit during the summer.
For the less mundane, the color-changing lends to differing characteristics of the water. Hook or plot drivers may entail collecting water at certain times, in order to gain certain abilities or characteristics - for more complexity, multiple trips may be required, or only when two or more of the lakes are in a certain color combination. Of course, lake characteristics change randomly. Water qualities include curative, poisonous, component for potion or construct, toxin or other reactant specific to the big-bad or a barrier, etc. Have at it.