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During two sampling seasons we analyzed on weekly basis fatty acid (FA) composition of seston fraction 130μm, and compared them using a multivariate canonical correlation analysis (CCA). Besides, we evaluated a possible impact of water temperature and inorganic nutrients on FA composition of the seston and the zooplankton.In spite of significant differences in percentages of several individual FAs, we found very strong canonical correlation (cross-correlation, 1-week lag) between FA composition of the seston and the zooplankton. The most important factor, providing the overall canonical cross-correlation between FA profiles of the seston and the zooplankton fractions was eicosapentaenoic acid (20:5ω3, EPA). FA composition of the zooplankton fraction had comparatively poor correlations with taxonomic composition of the zooplankton. Thus, seasonal variations of FA composition of the zooplankton were determined primarily by seasonal changes in FA composition of the seston, rather than by taxonomic differences of FA profiles between rotifers, cyclopoids and cladocerans. FA composition of the seston was strongly affected by its taxonomic composition, namely by that of phytoplankton. According to CCA, the highest factor loadings pertained to diatoms interacting with their marker acids, including EPA, and cyanobacteria and greens, interacting with their marker acids. Ciliates and small rotifers composed considerable and sometimes major part of the seston biomass, but according to CCA their contributions to seasonal variations of the total FA profile of the seston were insignificant. This finding indirectly support the conclusion of the other authors, that the main source of FAs presented in ciliates and rotifers must be sought in algae and that they do not modify FA composition of food consumed, apart from repackaging it.Water temperature was the principal environmental parameter which drove the overall variations of FA composition. Factor loadings for the inorganic nutrients were comparatively negligible. The main contribution in the seasonal variation of FA composition of the seston was given by negative interaction between water temperature and percentage of EPA in the seston.