The "Supporting Healthy Interstate Fisheries in Transition Act" (SHIFT Act) is designed to modernize U.S. fishery management by addressing the impacts of dynamic ocean conditions and shifting fish stocks. It amends the Atlantic Coastal Fisheries Cooperative Management Act to require the Secretary of Commerce to encourage the inclusion of ecosystem change data in coastal fishery management plans. Specifically, when establishing or revising quota allocations, the Secretary must account for ecological changes, such as shifts in fish abundance, distribution, and potential food web or habitat impacts. The bill also significantly amends the Magnuson-Stevens Fishery Conservation and Management Act. It establishes a new process for the Secretary to determine when a substantial portion of a fishery extends beyond the geographical authority of a single Council , based on indicators like stock distribution shifts or changes in fishing effort or revenue. If such a shift is confirmed, the affected Councils must either designate one Council or agree to jointly prepare a fishery management plan or amendment within specified timelines. Should the Councils fail to reach an agreement, the Secretary is empowered to make the designation or mandate joint preparation. Furthermore, the SHIFT Act revises the process for authorizing new fisheries or fishing gear. It mandates that any proposed new fishery or gear must undergo a Council analysis demonstrating minimal adverse effects on essential fish habitat, existing fisheries, fishing communities, and the marine ecosystem. Councils are required to review their authorized lists every five years and propose necessary changes, with the Secretary making final determinations. The bill also allows for limited interim experimental fishing permits to gather crucial data for developing new management plans. Finally, the Act requires the Secretary of Commerce to submit a report to Congress every five years on its implementation, including metrics on resolved transboundary fisheries and the integration of ecological data. The provisions of this Act and its amendments will take effect 180 days after its enactment.