Tropical (warm) waters are clear because they support much less biomass.
http://www.gma.org/herring/biology/distribution/comparing_oceans.asp
http://www.gma.org/herring/biology/distribution/comparing_oceans.asp
This is because the higher temperature liberates the dissolved oxygen into the atmosphere, leaving less oxygen in the ocean to help support life.
"The solubility of oxygen, or its ability to dissolve in water, decreases as the water's temperature and salinity increase."
http://oceanservice.noaa.gov/education/kits/estuaries/media/supp_estuar10d_disolvedox.html
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