Species composition, structure and ecological characteristics of the vegetation of two pond types with different management, fishponds and storage ponds, in the Českobudějovická pánev basin (South Bohemia), were compared. A selection of 99 relevés from fishponds and 99 from storage ponds (small ponds used for the storage of marketable fish) made in 2000–2004 were analysed using direct and indirect ordination and ANOVA. The difference between storage ponds and fishponds was found to be more important than gradients correlated with temporal changes, soil moisture and mud depth. Storage ponds had a significantly higher mean number of species, bryophytes, archaeophytes and neophytes and beta-diversity. There were no significant differences in cover values, except of moss layer, which had significantly higher cover in storage ponds. Fishponds had significantly higher mean Ellenberg indicator values for light, continentality, moisture and nutrients. Oenanthe aquatica and Rumex maritimus are typical fishpond species and Amblystegium humile and Eleocharis palustris agg. typical storage pond species. The management of storage ponds is more varied and of different intensity than that of fishponds. It is assumed that management is a crucial factor determining the species richness and influencing the vegetation of these two habitats.