The Hudson River estuary, or the lower Hudson as it is sometimes called, begins where the tidal influence is first felt at Troy, New York, 240 kilometers (km) north of the Battery. From this point, the combined discharge of the upper Hudson and Mohawk rivers collects additional water from the drainage basins of twenty other, smaller tributaries. The intrusion of salt water is limited to the lower reaches and can extend 120 km above the Battery at times of low freshwater discharge.

The estuary acts as a machine for transporting sediment with two special, estuarine features. The first of these is the reversing tidal current. The Native American name for the Hudson is roughly translated as the "river that flows both ways." This tidal influence reaches all the way to the dam at Troy. Sediment introduced to the estuary is transported by tidal currents. Sand is usually moved near the estuary floor and sand transport can be recognized by the occurrence of ripples, or larger sand waves on the bottom. Because of the tidal conditions, sand is sometimes moved up the estuary and sometimes down.

The second distinguishing character of the estuarine sedimentary system is its relationship to the geochemical estuary, that is, the region of circulation of salty water. More dense, more saline water flows into the estuary at the sea floor while fresher, less dense surface water flows out to the sea. Within the geochemical estuary, fine-grained, suspended sediment is redistributed into turbidity maxima; that is, a region from which the concentration of suspended sediment decreases both upstream and downstream. Because of the landward circulation of bottom water, a marine source of sediment is likely. Fine-grained sediment is transported as suspended load in the estuary and deposited, resuspended, and redeposited many times before it is permanently buried in sediment deposits or exported to the sea. The deposition of fine-grained sediment is rapid in dredged navigation channels creating the need for continued maintenance.

The processes by which this transport occurs are extremely variable and cannot be predicted with certainty. Some measurements are available to document the general characterization of these processes, but there is little information concerning their variability in time and space. These processes are considered below.

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