The composition of the vegetation of fishpond mires in the Třeboň Basin (Czech Republic) was studied in relation to temporal fluctuations in certain environmental factors. The water-table depth, water pH and electrical conductivity at 49 permanent plots were measured at approximately threeweek intervals from March to October 2003. Minimum, maximum, mean, median and variation in the above-mentioned environmental factors were correlated with vegetation composition. The most important environmental factors explaining the variation in vegetation were mean pH and maximum water-table level. Median conductivity increased with increase in waterlogging and eutrophication. Some seasonal trends in the dynamics of these parameters were observed. The lowest conductivity was in spring, increased continuously throughout summer and peaked in autumn. In contrast, water level decreased in summer, when evapotranspiration was greatest, and rose in autumn after heavy rainfall. The pH increased from March to June, then was stable and decreased at the end of summer. Seasonal trends were generally identical in all vegetation types. The fluctuations in the environmental factors were so considerable that they may influence the reliability of vegetation environmental analyses.