On geological time-scales (≥106 years), the global geochemical cycles of carbon and silicon are coupled by the drawdown of atmospheric CO2 through chemical weathering of Ca- and Mg-silicate minerals in continental rocks. Rivers transport the soluble products of weathering (cations, alkalinity and silicic acid) to the oceans, where they are utilized by marine ecosystems. On decadal to glacial–interglacial time-scales, however, large biotic fluxes and storages of Si within terrestrial and freshwater ecosystems need to be taken into account. Recent studies have emphasized the importance of Si-accumulating plants, which deposit significant amounts of amorphous hydrated silica in their tissues as opal phytoliths. These include grasses, sedges, palms, some temperate deciduous trees and conifers, and many tropical hardwoods. Landscapes dominated by accumulator plants, such as tropical rainforests, grasslands, herbaceous wetlands and bamboo forests, act as ‘silica factories’. Important ‘silica bioengineers’ in freshwater ecosystems comprise diatoms, sponges and chrysophytes. This paper reviews the biological role of Si in higher plants, the impact of vegetation on rates of chemical weathering, the fluxes of Si through catchment ecosystems, lakes and rivers, and the potential contribution of new geochemical and isotopic tracers to Si biogeochemistry. Multiproxy investigations of lake sediments will provide novel insights into past variations in Si biocycling from terrestrial to aquatic realms on 10–106 year time-scales. Copyright © 2008 John Wiley & Sons, Ltd.