The "Marine Fisheries Habitat Protection Act" amends the National Fishing Enhancement Act of 1984 to facilitate the conversion of inactive offshore oil and gas platforms and pipelines into artificial reefs. This initiative aims to enhance marine fish habitat and promote commercial and recreational fishing opportunities. The bill introduces a comprehensive framework for managing the decommissioning of these structures by allowing them to be "Reefed in Place" rather than fully removed. The legislation defines key terms such as "Artificial reef," "Decommissioning," and "Reef in Place," which involves abandoning, toppling, or partially removing a structure to maximize reef ecosystems while ensuring navigational safety. An "Inactive structure" is one no longer useful for operations or on an expired lease, which can become an "Eligible structure" if it hosts or could host an "Established reef ecosystem." An applicant, typically the responsible operator, can initiate the "Reef in Place" process by submitting a notice of intent. This triggers an assessment by the Director of the Bureau of Safety and Environmental Enforcement (BSEE) to evaluate the structure's ecological value and economic benefits. If deemed eligible, a "Reef Planning Area" is designated, and final approval is granted by the Secretary of the Interior once wells are plugged, hazards removed, and liability is transferred. A crucial provision allows states with artificial reef programs to enter agreements with applicants to assume responsibility and liability for approved structures. In exchange, the state receives funds from the applicant, not exceeding 50 percent of the cost savings gained by reefing instead of full removal, unless otherwise agreed. Upon state acceptance, the applicant is relieved of all responsibility and liability, which then transfers solely to the state for continued maintenance. The bill also prohibits the Secretary of the Interior from issuing removal orders for inactive structures during various stages of the reefing process, including the initial notice, assessment, and eligibility determination periods, up to three years post-eligibility. An exception exists if the structure poses a substantial and imminent threat to navigational safety or the marine environment. This Act explicitly preserves other existing reefing or decommissioning mechanisms and pipeline abandonment regulations.