Temporal variation in fen water chemistry was studied in the Western Carpathian flysch zone (Czech Republic, Slovakia). Ten sites representing particular spring-fen type (tufa-forming fens, rich fens, spring-fen meadows, rich Sphagnum-fens, poor Sphagnum-fens) were studied. Water chemistry was determined three times a year (spring, summer, autumn) for 3 years. Water pH and conductivity were the most stable of the measured variables. Na+, K+, Ca2+ and SO42- were also relatively stable. On the contrary, NO3-, Cl-, Fe, PO43- and redox-potential temporally varied. These fluctuating, unstable variables explained very low or insignificant amounts of the variation in plant species data in our study area, possibly because of their instability. The separation of sites along PCA axis is clearest in the ordination of the autumnal data set. Major vegetation types were separated in PCA even when data from all three seasons were pooled.