There are 136 Federal harbors within the Great Lakes Basin, with 745 miles of navigation channels. A "Federal" channel or harbor is one that has been authorized by Congress. Most of these navigation authorizations date from the early 19th century. These harbors and channels were constructed to serve commercial navigation, recreational navigation, or both.

Channels and harbors are maintained for safe navigation. The depths of channels vary with the types of traffic. The navigation channels on the Mississippi and Ohio Rivers are maintained at authorized depths of 9 feet, which is sufficient for the barges and cargo they carry on these rivers. In contrast, the Connecting Channels between the Great Lakes are maintained at depths of 30 feet for the ocean-going ships which carry ore, coal, and other cargos between domestic and international ports. The channels at a particular harbor may have depths up to 30 feet at the entrance with progressively shallower depths as one moves upstream. This is especially common at harbors where commercial navigation is concentrated near the river mouth while recreation traffic extends a distance upstream.

In order to maintain channels and harbors at safe depths, periodic dredging is required. Great Lakes harbors and channels are maintained by the Corps' districts in:

• Buffalo (harbors in New York, Pennsylvania and Ohio)
• Chicago (harbors in Indiana and Illinois)
• Detroit (harbors in Michigan, Wisconsin and Minnesota)

Dredging and the management of dredged material are an important function of Corps districts. Typically, about 4 million cubic yards of sediments are dredged by the Corps of Engineers each year from Great Lakes harbors and channels, the equivalent to 400,000 truck loads of soil. On average, the Corps of Engineers spends about $20 million dollars annually for dredging and dredged material management in the Great Lakes Basin. 

Dredged material is a term used to describe the material excavated from a river, harbor or lake by a dredge. In the case of maintenance dredging, the material is sediment that has accumulated in the channel bottom since the last time it was dredged. In rivers, these sediments are soils that have been eroded from farmlands, forests, and gardens or washed off city street and carried by the water before depositing in a deepened channel. In the harbors and entrance channels that extend out into the lakes, the sediments are sand and silts that have been carried along the lake shoreline by littoral currents and deposited in the deepened channel. Over 90% of the dredged material is a clean soil that is physically and chemically the same as the soil on a field or in the park. The other ten percent may have contaminants that came from a number of possible sources including urban runoff and sewer overflows.

Sediments dredged from Great Lakes harbors and channels may be managed using one of the following methods:

• Open water placement (placement directly in the lake or river)
• Beach nourishment (placement on the beach or in the nearshore area)
• Capping (placement on the bottom of a lake and covering with clean material)
• Upland beneficial use (use for construction fill, landscaping, landfill cover, etc)
• Confined disposal (placement in a CDF or licensed landfill)
• Treatment (applying one or more processes to remove or destroy contaminants.

​The selection of the appropriate option for managing a dredged material is based on the type and level of contaminants present (if any), the volume of materials, local conditions, and environmental, social and economic factors.  The Corps is required to use the disposal alternative that is least costly and complies with applicable environmental laws and regulations. 

About half of the sediments dredged from Great Lakes harbors and channels are clean sand and silt than can be safely placed into the lakes, used to nourish beaches or for upland beneficial uses.  The other half contains levels of pollutants that restrict their disposal to some degree. 

Guidance developed jointly by the USEPA and Corps is used to determine which disposal methods are environmentally acceptable. 

• The Technical Framework is a national guidance manual developed by the Corps and USEPA that outlines the process for evaluating all possible management options for dredged material.
• The Great Lakes Dredged Material Testing & Evaluation Manual is a regional guidance manual used for determining if a dredged material is suitable for placement in the Great Lakes. Developed by the USEPA and Corps, the manual is for use by ports, marinas, governmental agencies, consultants, and laboratories in evaluations conducted under Section 404(b)(1) of the Clean Water Act.

Confined disposal facilities. A confined disposal facility, or CDF, is a structure planned and designed to receive sediments dredged from a navigation channel and safely contain the contaminants, preventing their reentry into the waterway or lake.The U.S. Army Corps of Engineers and Environmental Protection Agency have completed a report that provides a detailed summary of the 45  confined disposal facilities that have been used to manage contaminated sediments dredged from harbors and channels throughout the Great Lakes.

Environmental dredging. Contaminated sediments have been identified as a significant environmental problem in the Great Lakes and have been linked to the impairment of beneficial uses of Great Lakes waters at every one of the Areas of Concern designated in the Great Lakes Water Quality Agreement. Contaminated sediments have been dredged for environmental remediation at more than 30 Great Lakes sites. At many other sites with contaminated sediments, remediation efforts have become stalled for lack of funding, resources or other reasons.