A spokesman for the Sitka Sound Science Center says the water is red because of a plankton bloom.
Paul Norwood says on the center's website that he took a sample from Eastern Channel and found a plankton species common to the waters of Southeast Alaska.
He says it's not toxic to people but its blooms may produce enough ammonia to harm fish.
DEC environmental health officer Greg Johnstone tells the Sitka Sentinel that he was alerted to the bloom by his parents. They told him they hadn't seen such a thick bloom since arriving in the early 1940s.
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