Flowing water cleanses the water in that area because it moves away debris, whether litter or natural organic matter like sticks and leaves and inorganic matter like silt and peddles. Stationary water does not move much so debris piles up and makes the water stagnant. This water is very important for many species of invertebrates, some tadpoles, and various types of algae. It may appear dirty, but it is an important niche.
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