As the water slightly cools other forms of bacteria develop long hair-like strands which become visible to the naked eye. Only the first millimeter of a microbial mat actively grows. The top bacteria layer shades the bacteria below and new individuals grow upon the remains of the previous generation, thus forming a laminated mat. Thus, water chemistry and temperature determine the species present in a run-off channel. Pigments within microorganisms are responsible for their colors.
Chlorophyll produces grass-green, carotenoids are yellow, orange or red.
And all pigments found in living cells intensify or become muted directly by the amount of light they receive daily or seasonally. Large hot pools also radiate with brilliant colors ranging from deep blue to emerald green. These waters reflect the blue color rays present in sunlight and absorb the remainder of the color spectrum. A blue hot pool changes its mood from day to day, depending upon the intensity of light or the amount of particulate matter suspended in the water. Fine particles of silica or clay suspended in the water produce a baby blue colored pool, a blue thermal pool lined with yellow sulfur or yellow bacteria produces hues of green, forming emerald-colored pools.