Phosphorus (P) retention is an important ecosystem service provided by sediments and soils. However, when shallow aquatic sediments and poorly drained soils dry and re-flood, they can be a source, rather than a sink, of P. Using experimental drying and re-flooding in the laboratory, we assessed the resultant sediment–water P exchange in a biogeochemically diverse set of sediments from 16 sites in Michigan. The direction and magnitude of P exchange to pore waters and surface waters upon re-flooding varied among sediments. Different sediment properties were related to P release to pore water than to P release to overlying surface water, suggesting that different processes control two phases of sediment P release: mobilization from solid to dissolved forms in the sediment pore water; and movement of dissolved P from pore water into overlying surface water. We observed especially high P release in dried and re-flooded sediments with high amounts of loosely sorbed phosphate, suggesting that drained sediments with a legacy of high P loads will be most likely to release P and experience internal eutrophication when re-flooded. The differential responses of sediments suggest that aquatic ecosystem restoration and management for nutrient removal must be evaluated with site-specific knowledge of sediment and soil biogeochemistry.