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Porewater phosphate levels in submersed macrophyte grassbeds varied among years in the upper Chesapeake Bay (Maryland, USA) coincident with macrophyte species variation during these same years (1990, 1993, 1995). When native, deep-rooted Vallisneria americana Michx. was a codominant in the grassbed, the porewater phosphate concentrations were significantly lower (P < 0.001) than concentrations when the exotic, shallow-rooted species Hydrilla verticillata (L.f.) Royle and Myriophyllum spicatum L. were codominants. There were significant relationships (P < 0.001) between solid-phase inorganic phosphorus and reactive metals (Fe, Mn) in both native and exotic grassbeds. However, the slopes of the regression relationships between years were significantly different (P < 0.001), suggesting greater retention of inorganic phosphorus in sediments when V. americana was a codominant at the site. In addition, significant relationships between reactive manganese and iron in the sediments were observed, but the coefficient of determination was statistically greater (P < 0.001) when V. americana was a codominant at the site. Furthermore, plant cores of V. americana and H. verticillata had noticeably different sediment redox profiles, with the oxidation-reduction status of V. americana sediments being more oxidized in the root zone (i.e., +125 mV vs −5 mV at 4 cm depth). These data suggest that macrophyte species composition can alter sediment biogeochemistry resulting in varying porewater phosphate and solid-phase phosphorus and metal levels. Possible explanations for these biogeochemical differences may be attributed to morphological differences among macrophyte species (i.e., root/shoot ratio, canopy type, growth form) and differences in root oxygenation capabilities.