I came across an interesting article  at the Argentina's government Consejo Nacional de Investigaciones Científicas y Técnicas (National Council for Scientific and Technical Investigations), published a few days ago (Sept. 3, 2010).
It says that about ten days ago (around Aug. 25), Lake Huechulafquen's color changed and is no longer colored deep blue but instead it is turquoise. Locals are worried and asked CONICET to investigate the matter.
Some neighbors have said that a similar phenomenon happened in the 1970s after an earthquake in the area. Yet other locals have said that they never saw anything like it before.
This change in color has not affected two small lakes (Paimún -see my post on its Lake creature- and Epulafquen) which are joined to Huechulafquen's main body (they are actually two long fjords or arms of the main lake.
This lake is home to a Lake Cow and a lake monster known as Huechulito.
Samples taken from streams that flow into the lake show normal parameters. In my opinion they are looking in the wrong place.
Perhaps the cause of the strange color is volcanic activity by Lanín volcano, which stands over the lake with its beautiful cone. Though inactive, it may be belching gases into the lake's bed. There are hot water springs on the southern side of the lake, close to Lake Epulafquen.
A little googling shows that volcanic lakes take on a turquoise hue due to minerals in the water that reflect / refract light differently to pure water causing it to shift color. An example of this is Lake Poas in Costa Rica.
Furthermore another article clearly states that: "One feature of volcanic lakes influenced by subaqueous fumaroles existing at lake bottoms (called active crater lakes) is the remarkable color of their waters: turquoise or emerald green."
Lets hope that these changes (i.e. lower ph due to increased acidity) do not harm the local fauna and especially the cryptids.
UPDATE - Sept. 20, 2010
The CONICET experts have said that their preliminary findings indicates that the color of the lake may be due to sediments from the lake's bed blending into the water due to recent earthquakes in Chile. They are going to analyze samples taken from the lake which may take some time.
 Ohsawa Shinji et al. (2010) Color change of lake water at the active crater lake of Aso volcano, Yudamari, Japan: is it in response to change in water quality induced by volcanic activity? Limnology. 2010, vol. 11, no3, pp. 207-215
Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia2010 International Year of Biodiversity Copyright 2009-2010 by Austin Whittall ©