Dense surface canopies of aquatic macrophytes were associated with significant changes in the physical and chemical water quality of two shallow Pacific Northwest lakes. Internal loading of phosphorus (P) was observed at the sediment-water interface beneath canopies ofCeratophyllum demersumL. andMyriophtllum exalbescens(Fern.) Jeps. and in deep open-water areas when dissolved oxygen (DO) concentrations were ≤0.4 mg/L. Aerobic release of P was observed at sites with surface covers of the green filamentous algaePithophorasp. where concentrations of DO were >20 mg/L and pH >9. An increase in surface P concentrations was also observed in sites dominated by the floating leafedBrasenia schreberiGmel., and appeared to be associated with leaf decay within the surface canopy. There was an apparent net loss of phosphorus to the sediments beneath both submergent and floating leafed canopies when DO concentrations were ≥0.4 mg/L. The removal or reduction of the plant canopies could simultaneously reduce anoxic P release, while increasing aerobic P release. These P cycling mechanisms should be considered in the management of aquatic macrophytes.