Normally the natural courses of waters are protected and subject to control by government bodies' authorities. So every kind of work that resides in the waterway and adjacent controlled zones use to need previous approval by such authorities, that will decide in what way if any such works can be performed.
Normally such kind of works are directed by civil engineers knowledgeable in what are the better ways to protect the public interests whilst enabling the intent of the works, meaning the part that needs to be issued an authorization or warrant. These professionals will be able to discuss with the chief of operations for the works the alternatives that can be pursued in the most efficient way, either to protect the waterways, banks and floodable areas or any other that may be feasible and of interest.
Dredging is the answer to retire unwanted materials in the rivers, and is a technology in itself. A consultant should prepare the necessary works to ensure the intent is properly attained.
In short, my advice is to as soon as possible contact professionals entitled to project and direct the works you may need to include in your plan of operations.