There are two things that I remember vividly from my visit to Crater Lake National Park namely Wizard Island and some of the bluest water found in the world. The water is also some of the purest that you will find anywhere. When researching the reason for why the color was so blue, I found the answer on the National Park Service's website (paraphrased in the next paragraph).
The water is so blue because there is hardly anything else in it. The water molecules found in Crater Lake contain no sediments, algae, pesticides or pollution, making it very pure. The water molecules absorb all of the color spectrum of sunlight except for the blues. The key to creating the deep blue color is having enough water to absorb the other colors. Since there are 4.6 trillion gallons of water in the lake, there is no problem.