Section 10. The department shall have general care and supervision of the harbors and tide waters within the commonwealth, of the flats and lands flowed thereby, of the waters and banks of the Connecticut river and the banks and waters of the non-tidal portion of the Merrimack river and of all structures therein, in order to prevent and remove unauthorized encroachments and causes of every kind which may injure said Connecticut river or said part of Merrimack river or interfere with the navigation of such harbors, injure their channels or cause a reduction of their tide waters, and to protect and develop the rights and property of the commonwealth in such waters, flats and lands; and it may make such surveys, examinations and observations as it deems necessary therefor. The department of environmental protection shall protect the interests of the commonwealth in areas described herein in issuing any license and permit authorized pursuant to this chapter.