The commissioner may establish, along any tidal or inland waterway or flood-prone area considered for stream clearance, channel improvement or any form of flood control or flood alleviation measure, lines beyond which, in the direction of the waterway or flood-prone area, no obstruction, encroachment or hindrance shall be placed by any person, and no such obstruction, encroachment or hindrance shall be maintained by any person unless authorized by said commissioner. The commissioner shall issue or deny permits upon applications for establishing such encroachments based upon his findings of the effect of such proposed encroachments upon the flood-carrying and water storage capacity of the waterways and flood plains, flood heights, hazards to life and property, and the protection and preservation of the natural resources and ecosystems of the state, including but not limited to ground and surface water, animal, plant and aquatic life, nutrient exchange, and energy flow, with due consideration given to the results of similar encroachments constructed along the reach of waterway. Each application for a permit shall be accompanied by a fee as follows: (1) No change in grades and no construction of above-ground structures, four hundred seventy dollars; (2) a change in grade and no construction of above-ground structures, nine hundred forty dollars; and (3) a change in grade and above-ground structures or buildings, four thousand dollars.