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Abstract: We analysed the submerged soil seed bank of three fishponds in the Waldviertel region in Austria. We aimed our study at comparing the efficiency of two methods in detecting seeds quantitatively from soil samples of four characteristic mud-flat species, i.e. Carex bohemica, Coleanthus subtilis, Elatine hexandra, and Eleocharis ovata: the seedling-emergence and the rinsing method. Additionally, the actual vegetation was described based on 65 phytosociological relevés. Soil seed bank analyses were based on 31 samples representing the vegetation zonation. Mixed soil samples were portioned into 62 subsamples further treated with the two methods in parallel. Analysis of vegetation revealed a typical zonation with Isoëto-Nanojuncetea communities from the centre of dried-up fishponds to Phragmition/Magnocaricion communities at the shorelines. The study species were detected in the soil seed banks of all vegetation types, but seed abundances were generally higher in two fishponds characterised by muddy substrate than in one sandy mesotrophic pond (with the exception of E. hexandra). Therefore beside the water regime and the vegetation cover, additional factors such as soil type are likely to influence the soil seed bank composition of submerged sediments. The quantitative comparison of the seedling-emergence and the rinsing method revealed significantly higher seed numbers by the rinsing method. As we obtained 5.7 times (Elatine hexandra) to 17.5 times (Coleanthus subtilis) more seeds by rinsing, the averaged detection failure across the four study species was at least 89.7% with the seedling-emergence method. In addition to this advantage in the quantitative description of submerged soil seed bank compositions, the rinsing method enables us to use seeds subsequently for conservation management and revegetation purposes. [Copyright &y& Elsevier]