Wetland loss and increasing water scarcity in the Klamath Basin have reduced habitat availability for migratory waterbirds while intensifying competition among agricultural and conservation water uses. Although rotational wetland programs have been proposed as a strategy to integrate farming with habitat provision, their biogeochemical and ecological effects remain insufficiently quantified. This study evaluated how hydroperiod management influences phosphorus dynamics and habitat value across permanent wetlands, rotational wetlands, seasonal wetlands, and permanent agriculture. Soil and water samples were analyzed for phosphorus concentrations, and waterbird surveys were conducted to assess abundance, species richness, and community composition. Results showed that permanently cultivated agricultural fields contained the highest soil phosphorus concentrations, while rotational wetlands exhibited the highest phosphorus levels in surface waters, indicating mobilization of legacy phosphorus following flooding. Additionally, rotational wetlands supported the greatest waterbird abundance and species richness, comparable to or exceeding permanent wetlands. These findings demonstrate that rotational wetlands redistribute nutrients across soil and water pools while providing high-quality habitat for migratory birds. Overall, the results suggest that rotational wetland programs can simultaneously support agricultural productivity and waterbird conservation, offering a flexible management strategy for water-limited landscapes.