Intact sediment cores were taken from the deepest basins of 9 lakes in the Taupo Volcanic Zone, New Zealand, to investigate the factors controlling silicon (Si) concentrations in sediment pore waters and the flux of Si to the overlying lake water. The lakes ranged in trophic state from oligotrophic to highly eutrophic. A Si vertical flux model simulated Si gradients in the pore water with high precision (r2 0.95, p <0.01) in lakes with no volcanic tephra layers or significant geothermal inflows. The ubiquitous presence of diatom frustules in the sediment was likely responsible for release of Si to the pore waters and subsequent diffusion to overlying lake waters. Fluxes of Si were related to the trophic status of the lake and were greatest in eutrophic lakes where diatom populations reduced epilimnetic Si concentrations to <1 mg L−1. Temporal variations in the concentrations of Si, nitrogen (N), and phosphorus (P) suggest that over most of the year diatom growth in the oligotrophic lakes is limited by N, or co-limited by N and P. In some eutrophic lakes, Si may limit diatom growth during homothermal conditions, and P and/or N may limit growth when the lake is stratified. The reduction of surface Si concentrations to <0.1 mg L−1 following homothermy in some eutrophic lakes is likely to restrict the growth of diatoms, potentially resulting in increased dominance of nonsiliceous flagellated species and cyanobacteria.