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The significance of biogenic silicon (BSi) pools as a key factor for the control of Si fluxes from terrestrial to aquatic ecosystems has been recognized for decades. However, while most research has been focused on phytogenic Si pools, knowledge of other BSi pools is still limited. We hypothesized that different BSi pools influence short-term changes in the water-soluble Si fraction in soils to different extents. To test our hypothesis we took plant (<i>Calamagrostis epigejos</i>, <i>Phragmites australis</i>) and soil samples in an artificial catchment in a post-mining landscape in the state of Brandenburg, Germany. We quantified phytogenic (phytoliths), protistic (diatom frustules and testate amoeba shells) and zoogenic (sponge spicules) Si pools as well as Tiron-extractable and water-soluble Si fractions in soils at the beginning (<i>t</i>₀) and after 10 years (<i>t</i>₁₀) of ecosystem development. As expected the results of Tiron extraction showed that there are no consistent changes in the amorphous Si pool at Chicken Creek (<i>Hühnerwasser</i>) as early as after 10 years. In contrast to <i>t</i>₀ we found increased water-soluble Si and BSi pools at <i>t</i>₁₀; thus we concluded that BSi pools are the main driver of short-term changes in water-soluble Si. However, because total BSi represents only small proportions of water-soluble Si at <i>t</i>₀ (&lt; 2 %) and <i>t</i>₁₀ (2.8–4.3 %) we further concluded that smaller (&lt; 5 µm) and/or fragile phytogenic Si structures have the biggest impact on short-term changes in water-soluble Si. In this context, extracted phytoliths (&gt; 5 µm) only amounted to about 16 % of total Si contents of plant materials of <i>C. epigejos</i> and <i>P. australis</i> at <i>t</i>₁₀; thus about 84 % of small-scale and/or fragile phytogenic Si is not quantified by the used phytolith extraction method. Analyses of small-scale and fragile phytogenic Si structures are urgently needed in future work as they seem to represent the biggest and most reactive Si pool in soils. Thus they are the most important drivers of Si cycling in terrestrial biogeosystems.