We have studied the effect of the presence of emergent macrophytes on the sediment phosphate composition of a eutrophic shallow marsh on the NE margin of Doñana (SW Spain). Top sediment and water samples were collected from both the open-water and the vegetated sites at three areas covered by different plant species: Scirpus maritimus, Juncus subulatus and Phragmites australis. The concentration of organic matter was significantly higher in the top sediment of sites covered by vegetation than in their adjacent open-water sites at the three vegetation areas. The P-fractional composition showed that the sediment was dominated by the inorganic P-fractions in all cases, reaching the highest concentration in the Ca-bound P-fraction (281–372 μg g⁻¹ d.w.). The sum of all P-fractions was significantly higher in the top sediment of the sites covered by J. subulatus and S. maritimus than in their adjacent open-water sites, and so were the org-P fraction extracted by hot NaOH and the concentration of phytate within this fraction. Deposition of plant material on the top sediment of areas vegetated by J. subulatus and S. maritimus explains these differences. The P-fractional composition of the seeds from J. subulatus showed that they contained a large proportion of organic P-fractions, particularly of the fraction extracted by hot NaOH (1868 μg g⁻¹ d.w., 85% of which was phytate). The presence of emergent macrophytes, therefore, influenced the distribution of P-fractions in the sediment depending on plant species. The P-bioavailability of shallow aquatic systems must be fully understood if wetlands are to be protected from further eutrophication.