NASA Earth Observatory gives this explanation:
The color of the water generally depends on the amount and type of sediment, as the green, tan, and deep brown areas have varying degrees of suspended silt, sand, mud, leaf tannins, and other organic matter. Note, for instance, the darker brown tinting near the Passaic River in New Jersey (image left). The brightness, or reflectance, of the water is also an indication of how close to the top of the water column those sediments are moving.
It is also possible that phytoplankton are blooming in the wake of the storm. Waterborne sediment can block some of the sunlight for aquatic plants, but the stirring of the river bottom and the runoff from land brings massive amounts of nutrients to the water’s surface. The fresh water can stratify, or layer, the water column so that plankton can flourish at the surface without mixing downward.
In addition to soil and sand, flooding rivers can carry sewage, pesticides, and excess fertilizer. Researchers from the U.S. Geological Survey and other institutions are collecting samples to determine the amount of pesticides, fertilizer, E. coli and other bacteria, and sediment in the water. All can contribute to poor water quality and promote algae blooms that increase costs of treating drinking water. The movement of sediment also can affect coastal shipping channels.