To propose a concept of their mutual diversity, twenty-nine permanent shallow floodplain pools and oxbows in the river Lužnice floodplain were analysed for area, depth, shape, flooding, and shading by terrestrial vegetation, and sampled in all seasons for their water chemistry, phytoplankton composition and biomass, and zooplankton composition. The sites are regularly flooded, eutrophic, and often shaded by surrounding vegetation. Cryptophyceae, Chrysophyceae and Euglenophyceae dominated the phytoplankton, while Cyanophytes were rare. Within the rich zooplankton assemblage (63 species), cladocerans and rotifers dominated. Correlation matrices and multivariate analyses indicated that shaded and relatively deeper sites had lower oxygen saturation and higher concentrations of PO 4 -P and NH 4 -N. Shade and relative depth correlated negatively with phytoplankton biomass and number of phytoplankton taxa, and positively with Cryptophytes and large cladocerans-thus indicating poor mixing, poor light availability and low fish pressure on herbivores. Decomposition of leaf litter increased oxygen consumption, while shade from terrestrial vegetation restricted photosynthesis and decreased oxygen production. Larger sites were more species-rich in phytoplankton and supported Euglenophyceae, green algae and rotifers.