In hot water pools and springs most of the colours are due to bacteria, algae, minerals and the natural blue of water. Pools that are too hot to allow the growth of algae and bacteria are normally blue because the water, unaffected by alien growth, transmits only the blue of daylight reflecting from the pools’ geyserite sides and bottom. A example of this blue water can be found in the centre of Crested Glory Pool in Upper Geyser Basin.

In cooler pools where algae and bacteria can live the colour depends on the temperature and acidity of the water. In water of low, or no acidity, yellow algae indicate that the water is as hot as the algae can withstand. The yellow algae combine with the blue of the water to form green, as in Emerald Pool in Black Sands Basin. When temperatures drop in non-acidic water, orange and brown algae appear. In acidic waters, the algae that flourishes in high temperatures is bright green, such as Emerald Spring in Norris Geyser Basin. In cooler acidic waters, a purplish algae appears, then orange brown.

In running water such as Mammoth Hot Springs, temperatures lower rapidly as the water moves further from the source. Colours change rapidly. This is also true of run off waters from hot pools and geysers.

The cones edges and walls of hot springs and mud pots are coloured by minerals. Yellows are mostly sulphur. Oranges, reds, browns and blacks are from various forms of iron oxides and iron sulphides. Paint pots keep these minerals in suspension and frequently have a combination of minerals, resulting in their many varied colours.