The Pacific Flyway Habitat Enhancement Act amends the Food Security Act of 1985 to expand the Conservation Reserve Enhancement Program (CREP), specifically targeting the improvement of wetland wildlife habitats. It introduces new provisions for Seasonally Flooded Working Lands Habitat Conservation Agreements , allowing the Secretary of Agriculture to enroll additional agricultural land that might not typically be eligible if it is critical to addressing diminished wetland wildlife habitats. This legislation permits seasonally flooded agricultural uses on working cropland when maintaining habitat for wetland-dependent species, provided that at least one best management practice is adopted. The bill also modifies how annual rental payments are calculated, ensuring they are comparable with regional costs for similar habitats and maintain regional consistency. Additionally, the Secretary is granted the authority to waive the matching requirement for these specialized conservation agreements.