The Commissioner of Energy and Environmental Protection shall, on or before December 31, 2006, and after consultation and cooperation with the Department of Public Health, the Public Utilities Regulatory Authority, an advisory group convened by the Commissioner of Energy and Environmental Protection, and any other agency, board or commission of the state with which said commissioner shall deem it advisable to consult and after recognizing and providing for the needs and requirements of public health, flood control, industry, public utilities, water supply, public safety, agriculture and other lawful uses of such waters and further recognizing and providing for stream and river ecology, the requirements of natural aquatic life, natural wildlife and public recreation, and after considering the natural flow of water into an impoundment or diversion, and being reasonably consistent therewith, shall adopt regulations, in accordance with the provisions of chapter 54, establishing flow regulations for all river and stream systems. Such flow regulations shall: (1) Apply to all river and stream systems within this state; (2) preserve and protect the natural aquatic life, including anadromous fish, contained within such waters; (3) preserve and protect the natural and stocked wildlife dependent upon the flow of such water; (4) promote and protect the usage of such water for public recreation; (5) be based, to the maximum extent practicable, on natural variation of flows and water levels while providing for the needs and requirements of public health, flood control, industry, public utilities, water supply, public safety, agriculture and other lawful uses of such waters; and (6) be based on the best available science, including, but not limited to, natural aquatic habitat, biota, subregional basin boundaries, areas of stratified drift, stream gages and flow data, locations of registered, permitted, and proposed diversions and withdrawal data reported pursuant to section 22a-368a, locations where any dams or other structures impound or divert the waters of a river or stream and any release made therefrom, and any other data for developing such regulations or individual management plans. Such flow regulations may provide special conditions or exemptions including, but not limited to, an extreme economic hardship or other circumstance, an agricultural diversion, a water quality certification related to a license issued by the Federal Energy Regulatory Commission or as necessary to allow a public water system, as defined in subsection (a) of section 25-33d, to comply with the obligations of such system as set forth in the regulations of Connecticut state agencies. Any flow management plan contained in a resolution, agreement or stipulated judgment to which the state, acting through the Commissioner of Energy and Environmental Protection, is a party, or the management plan developed pursuant to section 3 of public act 00-152*, is exempt from any such flow regulations. Flow regulations that were adopted pursuant to this section and sections 26-141a and 26-141c prior to October 1, 2005, shall remain in effect until the Commissioner of Energy and Environmental Protection adopts new regulations pursuant to this section.