Diatom productivity in the oceans plays a crucial role in the carbon cycle, but is strongly dependent upon the continental silicon supply. However, the relative influence of weathering and biological processes on continental Si fluxes remains poorly constrained. This study aims to quantify the impact of terrestrial diatom productivity on Si fluxes to the ocean. Lake Myvatn in North Iceland is one of the most productive lakes in the Northern Hemisphere, with nutrient-rich waters almost uniquely sourced by groundwater. The primary production is mainly controlled by diatom growth but also by cyanobacteria, and the lake output is via a single river, thereby providing a relatively simple natural laboratory to quantify the impact of diatom growth on the chemistry and Si budget of lake waters. Silicon stable isotopes (δ30Si) provide a tracer of this biocycling, and have been measured in groundwater inputs to the lake, and in time-series monitoring of waters at the lake outlet. The δ30Si values at the outlet range from + 0.70 ± 0.08 to + 1.42 ± 0.06‰, which is significantly heavier than the groundwater input (average cold and hot springs: + 0.50 ± 0.17‰, 2SD) and consistent with the preferential uptake of light Si isotopes by diatoms. The δ30Si value at the outlet increases by up to 0.9‰ in spring and autumn relative to the Si isotope composition of the inflow. These seasonal diatom blooms can be modeled by an open system of Si uptake and affect Si fluxes at the outlet of the lake by up to 79%, or 53% integrated over the year. In the summer a shift to lighter δ30Si values is correlated with a higher pH, which results in dissolution of diatoms releasing light Si isotopes. From mass balance, this seasonal diatom dissolution affects Si fluxes by up to 33%, but is limited to 3.7% integrated over the year. These results clearly illustrate that biological activity can have a significant impact on both isotope composition and elemental abundance of continental derived Si. They also demonstrate the pH dependency of diatom dissolution and/or preservation, which is likely to affect not only the continental Si fluxes to the ocean but also the Si recycling in the oceans themselves.