AbstractThe stratification of two shallow and small pools, situated in a floodplain ecosystem, was investigated.A new methodological approach was applied. The parameter called summarized chemical and biological stratification (SCB), was derived from basic limnological parameters in order to evaluate the global intensity of chemical and biological stratification and to compare it with a thermal one.Three situations were described when the seasonal courses of thermal and SCB stratification were compared: 1. Both SCB and thermal stratification are present. 2. The water column is homogeneous — there is no stratification in the pool. 3. SCB stratification is present, but the water is homoiothermic. The thermal stratification is very unstable because of the small volume of the pools and frequent floods. The SCB stratification is of higher stability and it may persist in a homoiothermic water column. In comparison with temperate deep lakes, the thermal stratification does not play such an important role in initiating the chemical and biological stratification. The surface/volume ratio and the depth in the pools are lower, which cause the “bottom‐initiated” quick renovation of stratification even in homoiothermic water.The differences in oxygen regime, volume and localization of both investigated pools cause the differences in stratification patterns. Frequent oxygen depletions in one of the pools increase the intensity of stratification and influence its character. The anaerobic conditions lead to steeper gradients of basic nutrients, pH, alkalinity and water color.The occurrence of a unique phytoplankton community (Cryptophyceae) is probably closely related to the described stratification p