Back in the 1960's it was pretty much do what you want to do around Maine's waterways.

Bulldozer out in front of your cottage removing rocks that got in the way of your wharf..no problem. Dredge out the shoreline and dump sand or crushed gravel in to create the shoreline and lake bottom you want...go for it. Now we have gone from no regulation to layers of regulation on the federal, state and local levels. Maine law allows towns to enact more stringent ordinances and even ordinances that may differ from state guidelines. Best advice is to visit your town office and ask about the activity you wish to do and see if permit is needed and from who. If you are planning on building at a distance more than 100 feet back from a "great pond or river", remember harvesting operations can not create single clear cut openings greater than 10,000 square feet in the forest canopy. Where such openings exceed 5000 square feet they shall be at least 100 feet apart.  Also, there are many fine points to the shoreland regulations, but one important one to note is that in non-tidal areas the minimum lot size for residential dwelling units is 40,000 square feet with a minimum shore frontage of 200 feet. In tidal areas the lot size and frontage requirements are 30,000 square feet and 150 feet respectively.  The minimum set back for a new subsurface sewage disposal system must be no less than 100 feet from normal high water line. Before tackling a project around the water in Maine, see how the Shoreland Zoning, Natural Resources Protection Act, Erosion and Sedimentation Control Law and what your local town office or code enforcement official has for input and requirements.  Lots easier to do it right from the start then find out you are in violation later. Lots cheaper too! Read up on Maine Shoreland Zoning regulations...they are continually beefed up and changing.