Work within the waterways is highly regulated at the local, state and federal level. At the federal level more often than not a 404 permit is required for the work. The work can often be permitted under what the U.S. Army Corps of Engineers (USACE) refers to as nationwide permits which cover typical work within waterways. There are currently 52 nationwide permits which cover a wide range of types of works from dredging and bank stabilization to fish and wildlife harvesting or soil management for wildlife. Effective March 19, 2017 the USACE has reissued these permits which are effective for 5 years.
To find if your project may be covered by a nationwide permit the USACE has all permits and facts sheets listed at the below link with information on what they cover, how to obtain and other general information.