I know of a creek in Maine that arises in an oak bog. In the early spring the bog floods carrying water heavily contaminated with tannic acid from the decomposition of the previous autumns oak leaves. The creek drains across ultramafic ledge. When the tannic acid reacts with the iron oxide in the rock the creek turns as black as ink (Literally: I've written with it.) for two to three weeks.
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It could be dirt or some sort of pollution such as waste water from a treatment plant.
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Dirt in the water causes it too look black.
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Soil runoff is the most common cause.